Starting phenix.real_space_refine on Thu Feb 5 12:03:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtf_48607/02_2026/9mtf_48607.map" } resolution = 2.61 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10668 2.51 5 N 2908 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16961 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2511 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2519 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 301} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 960 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 960 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 960 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Time building chain proxies: 3.84, per 1000 atoms: 0.23 Number of scatterers: 16961 At special positions: 0 Unit cell: (126.431, 132.25, 152.881, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3304 8.00 N 2908 7.00 C 10668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 312 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 771.3 milliseconds 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3962 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 55 sheets defined 20.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 222 through 226 removed outlier: 4.232A pdb=" N ASP A 225 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.885A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.021A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 removed outlier: 3.588A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 127 removed outlier: 3.545A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.994A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.901A pdb=" N GLU E 78 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 193 through 202 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.727A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.031A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.595A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.506A pdb=" N ASP I 86 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR I 87 " --> pdb=" O THR I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.138A pdb=" N THR M 87 " --> pdb=" O THR M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53A removed outlier: 9.159A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 53 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.654A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 121A removed outlier: 4.129A pdb=" N SER A 117 " --> pdb=" O SER A 260A" (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 121A removed outlier: 4.129A pdb=" N SER A 117 " --> pdb=" O SER A 260A" (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.600A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.727A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 53A removed outlier: 5.816A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.601A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 121A removed outlier: 3.509A pdb=" N SER C 117 " --> pdb=" O SER C 260A" (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 115 through 121A removed outlier: 3.509A pdb=" N SER C 117 " --> pdb=" O SER C 260A" (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.660A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.656A pdb=" N THR D 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 32 removed outlier: 3.617A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD2, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD3, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.419A pdb=" N LEU E 51 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS E 284 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 53 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.680A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 118 through 125 removed outlier: 3.696A pdb=" N SER E 120 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 181 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 137 Processing sheet with id=AD7, first strand: chain 'E' and resid 142 through 147 removed outlier: 4.385A pdb=" N CYS E 145 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AD9, first strand: chain 'E' and resid 170 through 175 removed outlier: 3.585A pdb=" N ALA E 253 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 294 through 295 removed outlier: 4.145A pdb=" N CYS E 288 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.049A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.049A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.552A pdb=" N GLY I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.898A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.898A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'J' and resid 8 through 12 removed outlier: 6.616A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 8 through 12 Processing sheet with id=AF2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AF3, first strand: chain 'L' and resid 8 through 12 Processing sheet with id=AF4, first strand: chain 'L' and resid 8 through 12 Processing sheet with id=AF5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.148A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.148A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AF9, first strand: chain 'N' and resid 8 through 12 removed outlier: 6.573A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 8 through 12 714 hydrogen bonds defined for protein. 1887 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: 3.37 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5604 1.35 - 1.47: 4365 1.47 - 1.60: 7276 1.60 - 1.73: 0 1.73 - 1.86: 114 Bond restraints: 17359 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.328 1.438 -0.109 1.37e-02 5.33e+03 6.37e+01 bond pdb=" C SER F 124 " pdb=" N GLN F 125 " ideal model delta sigma weight residual 1.334 1.245 0.090 1.43e-02 4.89e+03 3.94e+01 bond pdb=" C GLN E 197 " pdb=" N ARG E 198 " ideal model delta sigma weight residual 1.334 1.248 0.086 1.46e-02 4.69e+03 3.47e+01 bond pdb=" C HIS C 130 " pdb=" N THR C 131 " ideal model delta sigma weight residual 1.331 1.407 -0.076 1.41e-02 5.03e+03 2.94e+01 bond pdb=" C ALA B 130 " pdb=" N LYS B 131 " ideal model delta sigma weight residual 1.330 1.399 -0.069 1.36e-02 5.41e+03 2.59e+01 ... (remaining 17354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 22854 2.35 - 4.70: 595 4.70 - 7.06: 83 7.06 - 9.41: 17 9.41 - 11.76: 1 Bond angle restraints: 23550 Sorted by residual: angle pdb=" CA PHE F 138 " pdb=" CB PHE F 138 " pdb=" CG PHE F 138 " ideal model delta sigma weight residual 113.80 120.72 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" CA HIS F 142 " pdb=" CB HIS F 142 " pdb=" CG HIS F 142 " ideal model delta sigma weight residual 113.80 120.46 -6.66 1.00e+00 1.00e+00 4.44e+01 angle pdb=" O GLY A 319 " pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 122.85 130.34 -7.49 1.20e+00 6.94e-01 3.90e+01 angle pdb=" N LEU C 320 " pdb=" CA LEU C 320 " pdb=" CB LEU C 320 " ideal model delta sigma weight residual 111.05 101.71 9.34 1.50e+00 4.44e-01 3.87e+01 angle pdb=" N THR C 318 " pdb=" CA THR C 318 " pdb=" C THR C 318 " ideal model delta sigma weight residual 113.88 106.26 7.62 1.23e+00 6.61e-01 3.83e+01 ... (remaining 23545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8938 17.99 - 35.98: 984 35.98 - 53.97: 285 53.97 - 71.96: 59 71.96 - 89.95: 27 Dihedral angle restraints: 10293 sinusoidal: 4054 harmonic: 6239 Sorted by residual: dihedral pdb=" CD ARG C 310 " pdb=" NE ARG C 310 " pdb=" CZ ARG C 310 " pdb=" NH1 ARG C 310 " ideal model delta sinusoidal sigma weight residual 0.00 80.88 -80.88 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -11.74 -74.26 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 21.68 71.32 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 10290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2142 0.069 - 0.137: 337 0.137 - 0.206: 31 0.206 - 0.275: 11 0.275 - 0.344: 5 Chirality restraints: 2526 Sorted by residual: chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA LEU C 320 " pdb=" N LEU C 320 " pdb=" C LEU C 320 " pdb=" CB LEU C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LYS D 131 " pdb=" N LYS D 131 " pdb=" C LYS D 131 " pdb=" CB LYS D 131 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2523 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 310 " 1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG C 310 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 310 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 310 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 310 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 50 " 0.836 9.50e-02 1.11e+02 3.75e-01 8.53e+01 pdb=" NE ARG N 50 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG N 50 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG N 50 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG N 50 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 315 " 0.785 9.50e-02 1.11e+02 3.52e-01 7.53e+01 pdb=" NE ARG C 315 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG C 315 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 315 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 315 " 0.024 2.00e-02 2.50e+03 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 63 2.51 - 3.10: 11766 3.10 - 3.70: 25665 3.70 - 4.30: 38739 4.30 - 4.90: 65368 Nonbonded interactions: 141601 Sorted by model distance: nonbonded pdb=" OG1 THR J 39 " pdb=" OE1 GLN J 42 " model vdw 1.908 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.180 3.040 nonbonded pdb=" O ASP F 19 " pdb=" OH TYR M 100G" model vdw 2.191 3.040 nonbonded pdb=" OG SER J 63 " pdb=" OG1 THR J 74 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR N 22 " pdb=" NZ LYS N 70 " model vdw 2.205 3.120 ... (remaining 141596 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 11 through 324) selection = (chain 'C' and (resid 11 through 79 or resid 81 through 324)) selection = (chain 'E' and (resid 11 through 80 or resid 82 through 331)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } 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: 36.170 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.000 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 17383 Z= 0.341 Angle : 0.868 11.760 23598 Z= 0.550 Chirality : 0.053 0.344 2526 Planarity : 0.016 0.488 3081 Dihedral : 16.737 89.955 6259 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.78 % Rotamer: Outliers : 2.01 % Allowed : 17.76 % Favored : 80.23 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.17), residues: 2156 helix: 1.41 (0.27), residues: 385 sheet: 0.33 (0.22), residues: 520 loop : -1.32 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 211 TYR 0.026 0.002 TYR J 49 PHE 0.018 0.002 PHE F 138 TRP 0.012 0.001 TRP A 84 HIS 0.011 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00582 (17359) covalent geometry : angle 0.86233 (23550) SS BOND : bond 0.00779 ( 24) SS BOND : angle 2.40119 ( 48) hydrogen bonds : bond 0.14739 ( 672) hydrogen bonds : angle 7.19072 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 400 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: B 131 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8248 (ptmm) REVERT: D 32 SER cc_start: 0.8671 (p) cc_final: 0.8383 (m) outliers start: 37 outliers final: 12 residues processed: 420 average time/residue: 0.7954 time to fit residues: 364.3883 Evaluate side-chains 405 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 392 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 50 ASN B 125 GLN C 48 ASN C 196 HIS D 25 HIS D 50 ASN D 125 GLN F 27 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 145 ASN N 95AASN N 96 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104836 restraints weight = 24199.983| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.77 r_work: 0.3315 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17383 Z= 0.234 Angle : 0.604 7.218 23598 Z= 0.318 Chirality : 0.045 0.255 2526 Planarity : 0.005 0.070 3081 Dihedral : 5.482 56.936 2383 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 3.64 % Allowed : 17.11 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.17), residues: 2156 helix: 1.54 (0.27), residues: 387 sheet: 0.44 (0.22), residues: 517 loop : -1.18 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 83 TYR 0.015 0.002 TYR F 34 PHE 0.017 0.002 PHE F 9 TRP 0.009 0.001 TRP N 35 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00543 (17359) covalent geometry : angle 0.59749 (23550) SS BOND : bond 0.00534 ( 24) SS BOND : angle 1.98429 ( 48) hydrogen bonds : bond 0.04936 ( 672) hydrogen bonds : angle 5.35570 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 381 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7579 (mp0) cc_final: 0.7378 (mp0) REVERT: A 93 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 194 LEU cc_start: 0.8201 (mt) cc_final: 0.7988 (mp) REVERT: C 77 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: C 79 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7676 (pp) REVERT: C 227 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7458 (mt-10) REVERT: E 44 GLU cc_start: 0.8184 (tp30) cc_final: 0.7941 (tp30) REVERT: E 76 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5870 (pt0) REVERT: E 109 GLU cc_start: 0.7966 (mp0) cc_final: 0.7582 (mp0) REVERT: F 77 MET cc_start: 0.8095 (mmm) cc_final: 0.7512 (mmm) REVERT: F 123 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8174 (tttp) REVERT: L 27 SER cc_start: 0.8924 (m) cc_final: 0.8640 (p) REVERT: N 70 LYS cc_start: 0.8371 (mtpm) cc_final: 0.7802 (mtpm) outliers start: 67 outliers final: 33 residues processed: 407 average time/residue: 0.7972 time to fit residues: 353.8992 Evaluate side-chains 410 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 372 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 148 optimal weight: 0.0980 chunk 117 optimal weight: 0.3980 chunk 79 optimal weight: 0.0870 chunk 212 optimal weight: 0.1980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 125 GLN D 50 ASN E 256 ASN E 276 ASN N 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106463 restraints weight = 24453.927| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.80 r_work: 0.3358 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17383 Z= 0.122 Angle : 0.527 8.137 23598 Z= 0.278 Chirality : 0.042 0.183 2526 Planarity : 0.004 0.060 3081 Dihedral : 4.785 40.363 2365 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 3.31 % Allowed : 17.49 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.17), residues: 2156 helix: 1.96 (0.27), residues: 384 sheet: 0.59 (0.23), residues: 485 loop : -1.04 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.010 0.001 TYR B 159 PHE 0.013 0.001 PHE B 9 TRP 0.008 0.001 TRP F 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00273 (17359) covalent geometry : angle 0.52410 (23550) SS BOND : bond 0.00438 ( 24) SS BOND : angle 1.39333 ( 48) hydrogen bonds : bond 0.04134 ( 672) hydrogen bonds : angle 4.99358 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 380 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8187 (mmtt) REVERT: C 77 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: C 224 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8074 (mmt180) REVERT: E 44 GLU cc_start: 0.8231 (tp30) cc_final: 0.7939 (tp30) REVERT: E 76 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5732 (pt0) REVERT: E 109 GLU cc_start: 0.7980 (mp0) cc_final: 0.7562 (mp0) REVERT: F 123 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8238 (tttp) REVERT: I 108 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: N 70 LYS cc_start: 0.8332 (mtpm) cc_final: 0.7662 (mtpm) outliers start: 61 outliers final: 33 residues processed: 411 average time/residue: 0.7378 time to fit residues: 331.5638 Evaluate side-chains 413 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 207 optimal weight: 0.4980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 125 GLN C 48 ASN C 196 HIS ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 256 ASN E 276 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN N 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104798 restraints weight = 24229.099| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.79 r_work: 0.3310 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17383 Z= 0.239 Angle : 0.586 9.006 23598 Z= 0.308 Chirality : 0.045 0.322 2526 Planarity : 0.005 0.059 3081 Dihedral : 5.019 43.024 2365 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 4.24 % Allowed : 17.93 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.17), residues: 2156 helix: 1.75 (0.27), residues: 387 sheet: 0.62 (0.23), residues: 485 loop : -1.03 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 211 TYR 0.015 0.002 TYR J 86 PHE 0.017 0.002 PHE F 9 TRP 0.009 0.001 TRP N 35 HIS 0.007 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00561 (17359) covalent geometry : angle 0.58013 (23550) SS BOND : bond 0.00580 ( 24) SS BOND : angle 1.94976 ( 48) hydrogen bonds : bond 0.04686 ( 672) hydrogen bonds : angle 5.07127 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 367 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.7641 (tp30) cc_final: 0.7112 (mp0) REVERT: C 77 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: C 79 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7643 (pp) REVERT: C 224 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8319 (mmt180) REVERT: D 131 LYS cc_start: 0.8630 (ptmm) cc_final: 0.8423 (ptmm) REVERT: F 123 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8201 (tttp) REVERT: I 108 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: L 27 SER cc_start: 0.8951 (m) cc_final: 0.8664 (p) outliers start: 78 outliers final: 47 residues processed: 405 average time/residue: 0.7376 time to fit residues: 325.9910 Evaluate side-chains 417 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 158 optimal weight: 0.0980 chunk 148 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 125 GLN C 196 HIS D 50 ASN E 276 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105285 restraints weight = 24098.453| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.78 r_work: 0.3317 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17383 Z= 0.177 Angle : 0.556 12.272 23598 Z= 0.293 Chirality : 0.044 0.267 2526 Planarity : 0.004 0.058 3081 Dihedral : 4.924 40.294 2365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 3.91 % Allowed : 18.63 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.17), residues: 2156 helix: 1.82 (0.27), residues: 387 sheet: 0.60 (0.23), residues: 485 loop : -0.99 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.011 0.001 TYR J 86 PHE 0.015 0.002 PHE F 9 TRP 0.008 0.001 TRP F 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00410 (17359) covalent geometry : angle 0.55035 (23550) SS BOND : bond 0.00549 ( 24) SS BOND : angle 1.77830 ( 48) hydrogen bonds : bond 0.04382 ( 672) hydrogen bonds : angle 4.97647 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: C 79 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7618 (pp) REVERT: C 224 ARG cc_start: 0.8608 (mmm160) cc_final: 0.8336 (mmt180) REVERT: D 131 LYS cc_start: 0.8624 (ptmm) cc_final: 0.8408 (ptmm) REVERT: E 281 MET cc_start: 0.7434 (tpt) cc_final: 0.7100 (tpt) REVERT: F 77 MET cc_start: 0.8120 (tpp) cc_final: 0.7734 (mmt) REVERT: F 123 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8264 (tttp) REVERT: I 108 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: M 108 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7444 (mp0) outliers start: 72 outliers final: 42 residues processed: 416 average time/residue: 0.7389 time to fit residues: 336.3597 Evaluate side-chains 424 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 59 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 166 optimal weight: 0.2980 chunk 124 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN C 48 ASN C 196 HIS D 50 ASN E 256 ASN E 276 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.118964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105678 restraints weight = 24197.635| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.79 r_work: 0.3325 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17383 Z= 0.153 Angle : 0.539 9.832 23598 Z= 0.285 Chirality : 0.043 0.240 2526 Planarity : 0.004 0.056 3081 Dihedral : 4.839 43.201 2365 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 3.80 % Allowed : 18.41 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.17), residues: 2156 helix: 1.87 (0.27), residues: 387 sheet: 0.58 (0.23), residues: 485 loop : -0.98 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.010 0.001 TYR B 159 PHE 0.015 0.001 PHE F 9 TRP 0.008 0.001 TRP F 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00353 (17359) covalent geometry : angle 0.53420 (23550) SS BOND : bond 0.00467 ( 24) SS BOND : angle 1.62254 ( 48) hydrogen bonds : bond 0.04167 ( 672) hydrogen bonds : angle 4.89142 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 380 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8088 (m) REVERT: B 29 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 143 LYS cc_start: 0.8589 (mttt) cc_final: 0.8286 (tttt) REVERT: C 77 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: C 79 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7581 (pp) REVERT: C 190 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: C 224 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8345 (mmt180) REVERT: C 227 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7523 (mt-10) REVERT: D 131 LYS cc_start: 0.8614 (ptmm) cc_final: 0.8376 (ptmm) REVERT: E 281 MET cc_start: 0.7442 (tpt) cc_final: 0.7155 (tpt) REVERT: F 59 MET cc_start: 0.7872 (tpp) cc_final: 0.7238 (tpp) REVERT: F 105 GLU cc_start: 0.7757 (tp30) cc_final: 0.7522 (tp30) REVERT: F 123 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (tttp) REVERT: I 108 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: M 108 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7427 (mp0) outliers start: 70 outliers final: 50 residues processed: 414 average time/residue: 0.7701 time to fit residues: 348.5566 Evaluate side-chains 435 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 161 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN C 196 HIS ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 276 ASN E 305 HIS F 125 GLN F 129 ASN N 96 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104948 restraints weight = 24082.943| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.78 r_work: 0.3312 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17383 Z= 0.213 Angle : 0.583 14.137 23598 Z= 0.305 Chirality : 0.045 0.275 2526 Planarity : 0.004 0.056 3081 Dihedral : 4.987 42.124 2365 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 4.02 % Allowed : 18.58 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.17), residues: 2156 helix: 1.73 (0.27), residues: 387 sheet: 0.60 (0.23), residues: 485 loop : -0.96 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.013 0.001 TYR J 86 PHE 0.017 0.002 PHE F 9 TRP 0.007 0.001 TRP N 35 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00500 (17359) covalent geometry : angle 0.57594 (23550) SS BOND : bond 0.00614 ( 24) SS BOND : angle 2.06343 ( 48) hydrogen bonds : bond 0.04441 ( 672) hydrogen bonds : angle 4.95788 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 369 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8188 (mtp85) REVERT: A 140 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8097 (m) REVERT: B 29 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 68 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: B 143 LYS cc_start: 0.8623 (mttt) cc_final: 0.8312 (tttt) REVERT: C 77 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: C 79 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7600 (pp) REVERT: C 227 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7536 (mt-10) REVERT: D 131 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8398 (ptmm) REVERT: E 201 TYR cc_start: 0.8352 (m-80) cc_final: 0.8123 (m-80) REVERT: F 105 GLU cc_start: 0.7772 (tp30) cc_final: 0.7553 (tp30) REVERT: F 123 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (tttp) REVERT: I 108 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: M 108 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7428 (mp0) outliers start: 74 outliers final: 48 residues processed: 408 average time/residue: 0.7682 time to fit residues: 342.0600 Evaluate side-chains 421 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 93 optimal weight: 0.3980 chunk 204 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 212 optimal weight: 0.2980 chunk 163 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN C 48 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 276 ASN F 125 GLN N 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104965 restraints weight = 24314.709| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.80 r_work: 0.3313 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17383 Z= 0.187 Angle : 0.570 11.700 23598 Z= 0.299 Chirality : 0.044 0.257 2526 Planarity : 0.004 0.056 3081 Dihedral : 4.968 43.354 2365 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 3.69 % Allowed : 19.34 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.17), residues: 2156 helix: 1.76 (0.27), residues: 387 sheet: 0.61 (0.23), residues: 485 loop : -0.94 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.011 0.001 TYR F 24 PHE 0.015 0.002 PHE F 9 TRP 0.007 0.001 TRP F 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00437 (17359) covalent geometry : angle 0.56432 (23550) SS BOND : bond 0.00620 ( 24) SS BOND : angle 1.91575 ( 48) hydrogen bonds : bond 0.04334 ( 672) hydrogen bonds : angle 4.92424 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 371 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 29 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 68 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: B 143 LYS cc_start: 0.8614 (mttt) cc_final: 0.8314 (tttt) REVERT: C 77 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: C 79 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (pp) REVERT: C 227 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7554 (mt-10) REVERT: D 2 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7617 (tm) REVERT: D 131 LYS cc_start: 0.8626 (ptmm) cc_final: 0.8387 (ptmm) REVERT: E 201 TYR cc_start: 0.8358 (m-80) cc_final: 0.8124 (m-80) REVERT: F 105 GLU cc_start: 0.7785 (tp30) cc_final: 0.7579 (tp30) REVERT: F 123 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8262 (tttp) REVERT: I 108 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: M 108 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7433 (mp0) outliers start: 68 outliers final: 49 residues processed: 407 average time/residue: 0.7031 time to fit residues: 313.1642 Evaluate side-chains 424 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 367 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 187 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 276 ASN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105311 restraints weight = 24126.176| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.79 r_work: 0.3318 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17383 Z= 0.159 Angle : 0.559 10.201 23598 Z= 0.293 Chirality : 0.043 0.237 2526 Planarity : 0.004 0.055 3081 Dihedral : 4.907 44.684 2365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 3.53 % Allowed : 19.93 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.18), residues: 2156 helix: 1.83 (0.27), residues: 387 sheet: 0.60 (0.23), residues: 485 loop : -0.92 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 211 TYR 0.013 0.001 TYR F 24 PHE 0.015 0.001 PHE F 9 TRP 0.008 0.001 TRP F 92 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00371 (17359) covalent geometry : angle 0.55350 (23550) SS BOND : bond 0.00599 ( 24) SS BOND : angle 1.88634 ( 48) hydrogen bonds : bond 0.04163 ( 672) hydrogen bonds : angle 4.87506 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 368 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8077 (m) REVERT: B 29 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 68 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8238 (mttp) REVERT: B 143 LYS cc_start: 0.8597 (mttt) cc_final: 0.8311 (tttt) REVERT: C 77 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: C 79 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7594 (pp) REVERT: C 190 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: C 227 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7551 (mt-10) REVERT: D 2 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7623 (tm) REVERT: D 131 LYS cc_start: 0.8617 (ptmm) cc_final: 0.8381 (ptmm) REVERT: E 201 TYR cc_start: 0.8360 (m-80) cc_final: 0.8133 (m-80) REVERT: F 59 MET cc_start: 0.7894 (tpp) cc_final: 0.7183 (tpp) REVERT: F 123 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7593 (tttp) REVERT: F 132 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7351 (mt-10) REVERT: I 108 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: M 108 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7424 (mp0) outliers start: 65 outliers final: 47 residues processed: 401 average time/residue: 0.7984 time to fit residues: 349.1495 Evaluate side-chains 430 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 374 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 173 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 190 optimal weight: 0.3980 chunk 160 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN E 256 ASN E 276 ASN F 125 GLN N 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105086 restraints weight = 24225.700| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.78 r_work: 0.3315 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17383 Z= 0.191 Angle : 0.578 10.031 23598 Z= 0.303 Chirality : 0.044 0.310 2526 Planarity : 0.004 0.055 3081 Dihedral : 5.016 45.543 2365 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 3.53 % Allowed : 20.15 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.18), residues: 2156 helix: 1.71 (0.27), residues: 387 sheet: 0.59 (0.23), residues: 485 loop : -0.93 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 81A TYR 0.015 0.001 TYR F 24 PHE 0.016 0.002 PHE F 9 TRP 0.007 0.001 TRP F 92 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00447 (17359) covalent geometry : angle 0.57132 (23550) SS BOND : bond 0.00633 ( 24) SS BOND : angle 1.95980 ( 48) hydrogen bonds : bond 0.04309 ( 672) hydrogen bonds : angle 4.90672 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (m) REVERT: B 29 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 68 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8240 (mttp) REVERT: B 143 LYS cc_start: 0.8598 (mttt) cc_final: 0.8322 (tttt) REVERT: C 77 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: C 79 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7610 (pp) REVERT: C 190 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: C 227 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 2 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7630 (tm) REVERT: D 131 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8402 (ptmm) REVERT: F 123 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8269 (tttp) REVERT: I 108 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: M 108 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7432 (mp0) outliers start: 65 outliers final: 47 residues processed: 413 average time/residue: 0.7870 time to fit residues: 355.1912 Evaluate side-chains 437 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 381 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 25 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 136 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN E 256 ASN E 276 ASN F 125 GLN N 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104880 restraints weight = 24130.859| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.78 r_work: 0.3315 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17383 Z= 0.200 Angle : 0.584 9.932 23598 Z= 0.306 Chirality : 0.045 0.260 2526 Planarity : 0.004 0.056 3081 Dihedral : 5.027 46.750 2365 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 3.42 % Allowed : 20.26 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.17), residues: 2156 helix: 1.67 (0.27), residues: 387 sheet: 0.58 (0.23), residues: 485 loop : -0.91 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 81A TYR 0.014 0.001 TYR C 161 PHE 0.016 0.002 PHE F 9 TRP 0.007 0.001 TRP F 92 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00469 (17359) covalent geometry : angle 0.57742 (23550) SS BOND : bond 0.00633 ( 24) SS BOND : angle 1.95689 ( 48) hydrogen bonds : bond 0.04336 ( 672) hydrogen bonds : angle 4.90759 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9299.62 seconds wall clock time: 158 minutes 55.18 seconds (9535.18 seconds total)