Starting phenix.real_space_refine on Fri Sep 19 09:01:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrx_48564/09_2025/9mrx_48564.map" } resolution = 3.75 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= 0.002 sd= 0.015 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 74 5.16 5 C 15665 2.51 5 N 3914 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24165 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1591 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1591 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain: "C" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1591 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1591 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain: "K" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "L" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "H" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "J" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "D" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "E" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "F" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2543 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Time building chain proxies: 5.44, per 1000 atoms: 0.23 Number of scatterers: 24165 At special positions: 0 Unit cell: (187.502, 187.502, 134.638, 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 74 16.00 O 4512 8.00 N 3914 7.00 C 15665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 38 " 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 28 sheets defined 45.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.550A pdb=" N LEU G 14 " --> pdb=" O GLY G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 42 through 50 Processing helix chain 'G' and resid 51 through 76 removed outlier: 3.972A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 102 Processing helix chain 'G' and resid 102 through 107 removed outlier: 3.724A pdb=" N MET G 106 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 107' Processing helix chain 'G' and resid 112 through 132 removed outlier: 4.228A pdb=" N LYS G 132 " --> pdb=" O ILE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 removed outlier: 3.689A pdb=" N PHE G 145 " --> pdb=" O THR G 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.790A pdb=" N ALA A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 50 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.034A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.644A pdb=" N MET A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 107' Processing helix chain 'A' and resid 112 through 132 removed outlier: 4.277A pdb=" N LYS A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.671A pdb=" N PHE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 50 through 76 removed outlier: 3.911A pdb=" N THR C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.553A pdb=" N LEU C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.041A pdb=" N MET C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 107' Processing helix chain 'C' and resid 112 through 132 removed outlier: 4.317A pdb=" N LYS C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.572A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.592A pdb=" N LEU I 14 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 50 through 76 removed outlier: 4.003A pdb=" N ILE I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR I 74 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR I 76 " --> pdb=" O ASN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.587A pdb=" N LEU I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 98 " --> pdb=" O SER I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 112 through 132 removed outlier: 4.244A pdb=" N LYS I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.710A pdb=" N ASN K 16 " --> pdb=" O LYS K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 56 Processing helix chain 'K' and resid 66 through 70 Processing helix chain 'K' and resid 86 through 97 removed outlier: 3.524A pdb=" N ASN K 90 " --> pdb=" O PRO K 86 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 192 removed outlier: 3.736A pdb=" N LEU K 189 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 214 removed outlier: 3.554A pdb=" N ILE K 199 " --> pdb=" O PHE K 195 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU K 214 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 226 Processing helix chain 'K' and resid 228 through 242 removed outlier: 4.293A pdb=" N LYS K 234 " --> pdb=" O SER K 230 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 260 removed outlier: 3.803A pdb=" N ILE K 253 " --> pdb=" O ASP K 249 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS K 260 " --> pdb=" O TYR K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 267 removed outlier: 3.770A pdb=" N ILE K 266 " --> pdb=" O TYR K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 292 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 37 through 56 Processing helix chain 'L' and resid 86 through 96 Processing helix chain 'L' and resid 107 through 111 removed outlier: 3.826A pdb=" N ASN L 110 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 192 Processing helix chain 'L' and resid 195 through 213 Processing helix chain 'L' and resid 219 through 225 Processing helix chain 'L' and resid 228 through 242 removed outlier: 4.147A pdb=" N LYS L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 259 removed outlier: 3.576A pdb=" N ILE L 253 " --> pdb=" O ASP L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 267 removed outlier: 3.608A pdb=" N ILE L 266 " --> pdb=" O TYR L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 292 Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 37 through 56 Processing helix chain 'H' and resid 86 through 97 removed outlier: 3.666A pdb=" N ASN H 90 " --> pdb=" O PRO H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.502A pdb=" N LYS H 111 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 192 removed outlier: 4.247A pdb=" N LEU H 189 " --> pdb=" O ASN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 214 removed outlier: 3.600A pdb=" N ILE H 199 " --> pdb=" O PHE H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 225 Processing helix chain 'H' and resid 228 through 242 removed outlier: 4.054A pdb=" N LYS H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 260 Processing helix chain 'H' and resid 280 through 292 Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 37 through 56 Processing helix chain 'J' and resid 86 through 96 Processing helix chain 'J' and resid 107 through 111 removed outlier: 3.881A pdb=" N ASN J 110 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 193 removed outlier: 3.596A pdb=" N LEU J 189 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 214 Processing helix chain 'J' and resid 219 through 225 Processing helix chain 'J' and resid 228 through 242 removed outlier: 4.430A pdb=" N LYS J 234 " --> pdb=" O SER J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 260 removed outlier: 3.598A pdb=" N ILE J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 267 removed outlier: 3.586A pdb=" N ILE J 266 " --> pdb=" O TYR J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 292 Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.502A pdb=" N ASN D 110 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 111 " --> pdb=" O PRO D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 195 through 212 removed outlier: 3.998A pdb=" N ILE D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.529A pdb=" N ALA D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 removed outlier: 3.567A pdb=" N ILE D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 267 removed outlier: 3.669A pdb=" N ILE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.544A pdb=" N ASN E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 56 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 86 through 97 removed outlier: 3.956A pdb=" N ALA E 97 " --> pdb=" O THR E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.845A pdb=" N VAL E 140 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 192 removed outlier: 3.794A pdb=" N LEU E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 214 removed outlier: 3.744A pdb=" N ILE E 199 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 228 through 242 removed outlier: 4.503A pdb=" N LYS E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.784A pdb=" N ILE E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.716A pdb=" N ILE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 Processing helix chain 'F' and resid 2 through 16 Processing helix chain 'F' and resid 37 through 56 Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.612A pdb=" N PHE F 70 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.612A pdb=" N ASN F 110 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 111' Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 195 through 214 removed outlier: 3.532A pdb=" N LEU F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 226 Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.933A pdb=" N LYS F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 259 removed outlier: 3.512A pdb=" N ILE F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 267 removed outlier: 3.580A pdb=" N ILE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 Processing sheet with id=AA1, first strand: chain 'G' and resid 82 through 88 removed outlier: 5.615A pdb=" N ILE G 84 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G 155 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER G 86 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE G 166 " --> pdb=" O PHE G 189 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA G 191 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE G 168 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS G 193 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 179 " --> pdb=" O VAL G 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.157A pdb=" N ILE A 166 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.682A pdb=" N VAL C 179 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.213A pdb=" N ILE C 166 " --> pdb=" O PHE C 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.511A pdb=" N VAL I 179 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 88 through 89 removed outlier: 6.240A pdb=" N ILE I 166 " --> pdb=" O PHE I 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 31 through 33 removed outlier: 3.632A pdb=" N GLY K 19 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG K 21 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY K 117 " --> pdb=" O THR K 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU K 174 " --> pdb=" O TYR K 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 268 through 269 removed outlier: 3.638A pdb=" N GLN K 268 " --> pdb=" O LEU K 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 295 through 297 Processing sheet with id=AB2, first strand: chain 'K' and resid 310 through 311 Processing sheet with id=AB3, first strand: chain 'L' and resid 31 through 33 removed outlier: 7.107A pdb=" N PHE L 17 " --> pdb=" O GLY L 124 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY L 124 " --> pdb=" O PHE L 17 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY L 19 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE L 122 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG L 21 " --> pdb=" O ILE L 120 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE L 120 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL L 23 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE L 118 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR L 25 " --> pdb=" O LYS L 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 143 through 144 Processing sheet with id=AB5, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.531A pdb=" N GLY H 117 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE H 120 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 174 " --> pdb=" O TYR H 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 268 through 269 removed outlier: 3.774A pdb=" N GLN H 268 " --> pdb=" O LEU H 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 295 through 297 Processing sheet with id=AB8, first strand: chain 'H' and resid 311 through 312 Processing sheet with id=AB9, first strand: chain 'J' and resid 31 through 33 removed outlier: 4.033A pdb=" N GLY J 19 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG J 21 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU J 174 " --> pdb=" O TYR J 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 142 through 144 Processing sheet with id=AC2, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.993A pdb=" N SER D 123 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 20 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU D 121 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL D 22 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 119 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE D 24 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY D 117 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 26 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL D 115 " --> pdb=" O THR D 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 268 through 269 removed outlier: 4.041A pdb=" N GLN D 268 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 295 through 297 Processing sheet with id=AC5, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.971A pdb=" N SER E 123 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY E 117 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.971A pdb=" N SER E 123 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 174 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 268 through 269 removed outlier: 3.826A pdb=" N GLN E 268 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 295 through 297 removed outlier: 6.444A pdb=" N ALA F 309 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS E 310 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER F 307 " --> pdb=" O LYS E 310 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 297 " --> pdb=" O GLN F 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.879A pdb=" N PHE F 17 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY F 124 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY F 19 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE F 122 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG F 21 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE F 120 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL F 23 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE F 118 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 25 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 143 through 144 1075 hydrogen bonds defined for protein. 3066 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: 3.62 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7128 1.34 - 1.46: 5046 1.46 - 1.58: 12300 1.58 - 1.70: 2 1.70 - 1.83: 125 Bond restraints: 24601 Sorted by residual: bond pdb=" N VAL K 140 " pdb=" CA VAL K 140 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N LEU E 138 " pdb=" CA LEU E 138 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.32e-02 5.74e+03 1.02e+01 bond pdb=" N PRO J 152 " pdb=" CA PRO J 152 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.08e+00 bond pdb=" N PRO L 152 " pdb=" CA PRO L 152 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.05e+00 bond pdb=" N PRO K 152 " pdb=" CA PRO K 152 " ideal model delta sigma weight residual 1.469 1.435 0.034 1.28e-02 6.10e+03 7.06e+00 ... (remaining 24596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 32657 3.30 - 6.59: 415 6.59 - 9.89: 85 9.89 - 13.19: 11 13.19 - 16.48: 9 Bond angle restraints: 33177 Sorted by residual: angle pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " pdb=" CD LYS A 45 " ideal model delta sigma weight residual 111.30 125.38 -14.08 2.30e+00 1.89e-01 3.75e+01 angle pdb=" CB LYS J 302 " pdb=" CG LYS J 302 " pdb=" CD LYS J 302 " ideal model delta sigma weight residual 111.30 124.60 -13.30 2.30e+00 1.89e-01 3.34e+01 angle pdb=" N ARG C 3 " pdb=" CA ARG C 3 " pdb=" C ARG C 3 " ideal model delta sigma weight residual 111.37 120.88 -9.51 1.65e+00 3.67e-01 3.32e+01 angle pdb=" C LEU E 313 " pdb=" CA LEU E 313 " pdb=" CB LEU E 313 " ideal model delta sigma weight residual 116.54 109.98 6.56 1.15e+00 7.56e-01 3.25e+01 angle pdb=" N PRO K 152 " pdb=" CA PRO K 152 " pdb=" CB PRO K 152 " ideal model delta sigma weight residual 103.25 97.51 5.74 1.05e+00 9.07e-01 2.99e+01 ... (remaining 33172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12679 17.99 - 35.99: 1810 35.99 - 53.98: 481 53.98 - 71.97: 74 71.97 - 89.97: 16 Dihedral angle restraints: 15060 sinusoidal: 6184 harmonic: 8876 Sorted by residual: dihedral pdb=" CA ALA F 139 " pdb=" C ALA F 139 " pdb=" N VAL F 140 " pdb=" CA VAL F 140 " ideal model delta harmonic sigma weight residual 180.00 -144.35 -35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CB CYS A 33 " pdb=" SG CYS A 33 " pdb=" SG CYS A 38 " pdb=" CB CYS A 38 " ideal model delta sinusoidal sigma weight residual 93.00 31.51 61.49 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS G 33 " pdb=" SG CYS G 33 " pdb=" SG CYS G 38 " pdb=" CB CYS G 38 " ideal model delta sinusoidal sigma weight residual 93.00 33.30 59.70 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 15057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2900 0.058 - 0.115: 740 0.115 - 0.173: 162 0.173 - 0.230: 19 0.230 - 0.288: 21 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA ARG C 3 " pdb=" N ARG C 3 " pdb=" C ARG C 3 " pdb=" CB ARG C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB ILE D 177 " pdb=" CA ILE D 177 " pdb=" CG1 ILE D 177 " pdb=" CG2 ILE D 177 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR H 136 " pdb=" CA THR H 136 " pdb=" OG1 THR H 136 " pdb=" CG2 THR H 136 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3839 not shown) Planarity restraints: 4162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL J 140 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C VAL J 140 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL J 140 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU J 141 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 30 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO G 31 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO G 31 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 31 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 151 " 0.062 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO J 152 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO J 152 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 152 " 0.049 5.00e-02 4.00e+02 ... (remaining 4159 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3630 2.76 - 3.30: 22475 3.30 - 3.83: 40828 3.83 - 4.37: 45633 4.37 - 4.90: 77885 Nonbonded interactions: 190451 Sorted by model distance: nonbonded pdb=" OG SER C 15 " pdb=" OD1 ASN C 139 " model vdw 2.228 3.040 nonbonded pdb=" O ILE I 129 " pdb=" OG1 THR I 133 " model vdw 2.240 3.040 nonbonded pdb=" OG SER G 15 " pdb=" OD1 ASN G 139 " model vdw 2.275 3.040 nonbonded pdb=" OG SER K 102 " pdb=" OD1 ASP K 104 " model vdw 2.276 3.040 nonbonded pdb=" O GLY H 19 " pdb=" OG SER H 123 " model vdw 2.282 3.040 ... (remaining 190446 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 10.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.005 0.084 24605 Z= 0.233 Angle : 0.985 16.485 33185 Z= 0.526 Chirality : 0.057 0.288 3842 Planarity : 0.008 0.129 4162 Dihedral : 17.644 89.968 9282 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 0.77 % Allowed : 28.04 % Favored : 71.19 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.85 (0.13), residues: 2963 helix: -1.42 (0.12), residues: 1226 sheet: -1.19 (0.26), residues: 416 loop : -2.54 (0.14), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 145 TYR 0.044 0.002 TYR A 181 PHE 0.057 0.002 PHE E 287 HIS 0.014 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00505 (24601) covalent geometry : angle 0.98542 (33177) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.47974 ( 8) hydrogen bonds : bond 0.14865 ( 1074) hydrogen bonds : angle 6.82291 ( 3066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 168 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7194 (mm) REVERT: H 287 PHE cc_start: 0.7103 (t80) cc_final: 0.6640 (t80) REVERT: H 291 MET cc_start: 0.7563 (mmm) cc_final: 0.6999 (mmm) REVERT: E 74 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7663 (mmtp) REVERT: F 306 MET cc_start: 0.6898 (tpp) cc_final: 0.6598 (ttm) outliers start: 21 outliers final: 5 residues processed: 244 average time/residue: 0.1584 time to fit residues: 59.4644 Evaluate side-chains 220 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN I 170 ASN K 16 ASN J 16 ASN E 59 ASN F 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.198090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165601 restraints weight = 38659.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163711 restraints weight = 60012.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161852 restraints weight = 54788.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161000 restraints weight = 54920.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 78)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160465 restraints weight = 50524.182| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 24605 Z= 0.131 Angle : 0.585 14.710 33185 Z= 0.305 Chirality : 0.043 0.151 3842 Planarity : 0.006 0.164 4162 Dihedral : 5.422 57.425 3211 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.88 % Favored : 92.95 % Rotamer: Outliers : 2.96 % Allowed : 25.52 % Favored : 71.52 % 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 aren not related in a simple way. whole: -1.72 (0.15), residues: 2963 helix: -0.01 (0.14), residues: 1234 sheet: -0.99 (0.27), residues: 416 loop : -2.32 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 145 TYR 0.021 0.001 TYR H 157 PHE 0.012 0.001 PHE E 175 HIS 0.008 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00314 (24601) covalent geometry : angle 0.58493 (33177) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.47829 ( 8) hydrogen bonds : bond 0.03915 ( 1074) hydrogen bonds : angle 4.88898 ( 3066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 235 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: A 159 SER cc_start: 0.8101 (t) cc_final: 0.7830 (p) REVERT: C 73 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7755 (tp) REVERT: K 177 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (tp) REVERT: L 168 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7007 (mm) outliers start: 81 outliers final: 40 residues processed: 291 average time/residue: 0.1622 time to fit residues: 73.3284 Evaluate side-chains 249 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 147 MET Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 128 CYS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 257 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 115 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 207 optimal weight: 0.3980 chunk 102 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 12 optimal weight: 0.5980 chunk 251 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN G 178 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 ASN K 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.198477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165769 restraints weight = 38712.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164863 restraints weight = 62105.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163629 restraints weight = 55587.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162904 restraints weight = 51412.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.162518 restraints weight = 49029.433| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24605 Z= 0.115 Angle : 0.546 8.901 33185 Z= 0.285 Chirality : 0.042 0.149 3842 Planarity : 0.005 0.137 4162 Dihedral : 5.035 54.768 3205 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.15 % Favored : 92.68 % Rotamer: Outliers : 3.50 % Allowed : 25.67 % Favored : 70.83 % 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 aren not related in a simple way. whole: -1.25 (0.15), residues: 2963 helix: 0.56 (0.15), residues: 1234 sheet: -0.91 (0.27), residues: 416 loop : -2.20 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 211 TYR 0.018 0.001 TYR H 157 PHE 0.013 0.001 PHE E 287 HIS 0.007 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00278 (24601) covalent geometry : angle 0.54545 (33177) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.78330 ( 8) hydrogen bonds : bond 0.03485 ( 1074) hydrogen bonds : angle 4.60025 ( 3066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 213 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: C 33 CYS cc_start: 0.5379 (OUTLIER) cc_final: 0.5176 (p) REVERT: C 73 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7669 (tp) REVERT: I 73 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8052 (mm) REVERT: K 172 TYR cc_start: 0.8123 (p90) cc_final: 0.7740 (p90) REVERT: K 177 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8440 (tp) REVERT: L 168 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 119 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8480 (mt) REVERT: J 105 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.4543 (m-80) outliers start: 96 outliers final: 43 residues processed: 284 average time/residue: 0.1581 time to fit residues: 71.3325 Evaluate side-chains 249 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 165 optimal weight: 0.0870 chunk 247 optimal weight: 0.4980 chunk 263 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN A 170 ASN A 178 ASN C 170 ASN I 170 ASN H 196 HIS ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.201470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158287 restraints weight = 41459.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155575 restraints weight = 61888.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154567 restraints weight = 46337.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.152681 restraints weight = 47964.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149468 restraints weight = 52446.399| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24605 Z= 0.183 Angle : 0.583 12.732 33185 Z= 0.304 Chirality : 0.044 0.157 3842 Planarity : 0.005 0.125 4162 Dihedral : 5.020 56.287 3203 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.63 % Favored : 92.20 % Rotamer: Outliers : 4.02 % Allowed : 25.85 % Favored : 70.14 % 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 aren not related in a simple way. whole: -1.14 (0.15), residues: 2963 helix: 0.66 (0.15), residues: 1241 sheet: -0.99 (0.26), residues: 436 loop : -2.13 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.025 0.001 TYR I 76 PHE 0.016 0.001 PHE H 287 HIS 0.008 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00457 (24601) covalent geometry : angle 0.58272 (33177) SS BOND : bond 0.00456 ( 4) SS BOND : angle 1.40136 ( 8) hydrogen bonds : bond 0.03645 ( 1074) hydrogen bonds : angle 4.61567 ( 3066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 204 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: C 73 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7783 (tp) REVERT: C 101 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: K 172 TYR cc_start: 0.8364 (p90) cc_final: 0.7853 (p90) REVERT: K 177 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8529 (tp) REVERT: K 308 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8344 (mt) REVERT: L 168 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7688 (mm) REVERT: H 119 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (mt) REVERT: J 105 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.4737 (m-80) outliers start: 110 outliers final: 61 residues processed: 289 average time/residue: 0.1658 time to fit residues: 75.8452 Evaluate side-chains 264 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 178 optimal weight: 0.0030 chunk 258 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 chunk 195 optimal weight: 30.0000 chunk 177 optimal weight: 0.1980 chunk 204 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN A 170 ASN K 186 HIS J 107 ASN J 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.198962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160828 restraints weight = 42203.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157541 restraints weight = 58939.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.156021 restraints weight = 48425.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.155256 restraints weight = 45960.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.153818 restraints weight = 38911.331| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24605 Z= 0.110 Angle : 0.534 10.491 33185 Z= 0.278 Chirality : 0.042 0.161 3842 Planarity : 0.005 0.117 4162 Dihedral : 4.850 56.095 3203 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.92 % Favored : 92.91 % Rotamer: Outliers : 3.18 % Allowed : 26.47 % Favored : 70.35 % 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 aren not related in a simple way. whole: -0.95 (0.15), residues: 2963 helix: 0.88 (0.15), residues: 1245 sheet: -0.96 (0.27), residues: 416 loop : -2.07 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 142 TYR 0.016 0.001 TYR G 76 PHE 0.020 0.001 PHE E 287 HIS 0.008 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00264 (24601) covalent geometry : angle 0.53358 (33177) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.97379 ( 8) hydrogen bonds : bond 0.03242 ( 1074) hydrogen bonds : angle 4.41272 ( 3066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 210 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: C 73 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7584 (tp) REVERT: C 101 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: K 172 TYR cc_start: 0.8273 (p90) cc_final: 0.7770 (p90) REVERT: K 177 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8495 (tp) REVERT: L 141 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7902 (pp) REVERT: L 211 ARG cc_start: 0.4396 (mmm160) cc_final: 0.3986 (mmm160) REVERT: H 119 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8491 (mt) REVERT: J 105 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.4748 (m-80) REVERT: J 134 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8423 (p0) REVERT: E 208 ASN cc_start: 0.8240 (t0) cc_final: 0.7950 (t0) outliers start: 87 outliers final: 53 residues processed: 280 average time/residue: 0.1666 time to fit residues: 73.5313 Evaluate side-chains 258 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 73 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 278 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN A 170 ASN K 186 HIS ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.198914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.160418 restraints weight = 42451.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.157667 restraints weight = 57591.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155127 restraints weight = 45632.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.154761 restraints weight = 44942.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.153379 restraints weight = 37818.335| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24605 Z= 0.116 Angle : 0.540 14.324 33185 Z= 0.280 Chirality : 0.043 0.185 3842 Planarity : 0.005 0.112 4162 Dihedral : 4.773 56.549 3203 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.19 % Favored : 92.64 % Rotamer: Outliers : 3.21 % Allowed : 26.54 % Favored : 70.24 % 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 aren not related in a simple way. whole: -0.85 (0.15), residues: 2963 helix: 0.98 (0.15), residues: 1245 sheet: -0.91 (0.27), residues: 416 loop : -2.04 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 211 TYR 0.017 0.001 TYR G 76 PHE 0.018 0.001 PHE H 287 HIS 0.009 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00284 (24601) covalent geometry : angle 0.54032 (33177) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.85187 ( 8) hydrogen bonds : bond 0.03178 ( 1074) hydrogen bonds : angle 4.33364 ( 3066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 212 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: C 73 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7552 (tp) REVERT: C 101 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6722 (m-10) REVERT: I 73 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8097 (mm) REVERT: K 172 TYR cc_start: 0.8287 (p90) cc_final: 0.7730 (p90) REVERT: K 177 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8526 (tp) REVERT: K 308 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8248 (mt) REVERT: L 141 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7934 (pp) REVERT: H 119 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8500 (mt) REVERT: H 291 MET cc_start: 0.7270 (mmm) cc_final: 0.7025 (mmm) REVERT: J 105 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.4835 (m-80) REVERT: E 208 ASN cc_start: 0.8230 (t0) cc_final: 0.7948 (t0) outliers start: 88 outliers final: 58 residues processed: 278 average time/residue: 0.1624 time to fit residues: 71.5587 Evaluate side-chains 268 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 162 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 237 optimal weight: 0.0020 chunk 27 optimal weight: 4.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN A 170 ASN C 170 ASN I 170 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.196817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.156959 restraints weight = 42323.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.155389 restraints weight = 56729.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152237 restraints weight = 44942.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151360 restraints weight = 50950.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150241 restraints weight = 42941.114| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24605 Z= 0.153 Angle : 0.572 13.795 33185 Z= 0.294 Chirality : 0.043 0.162 3842 Planarity : 0.005 0.111 4162 Dihedral : 4.811 57.962 3203 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.86 % Favored : 91.97 % Rotamer: Outliers : 3.36 % Allowed : 26.47 % Favored : 70.17 % 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 aren not related in a simple way. whole: -0.84 (0.15), residues: 2963 helix: 1.01 (0.15), residues: 1245 sheet: -0.96 (0.27), residues: 416 loop : -2.03 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 211 TYR 0.022 0.001 TYR G 76 PHE 0.016 0.001 PHE H 287 HIS 0.010 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00383 (24601) covalent geometry : angle 0.57193 (33177) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.78475 ( 8) hydrogen bonds : bond 0.03366 ( 1074) hydrogen bonds : angle 4.38284 ( 3066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 208 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7644 (tp) REVERT: C 101 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6894 (m-10) REVERT: K 172 TYR cc_start: 0.8335 (p90) cc_final: 0.7786 (p90) REVERT: K 177 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8563 (tp) REVERT: K 308 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8367 (mt) REVERT: H 119 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8535 (mt) REVERT: J 105 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.4926 (m-80) REVERT: E 208 ASN cc_start: 0.8289 (t0) cc_final: 0.8016 (t0) outliers start: 92 outliers final: 71 residues processed: 278 average time/residue: 0.1633 time to fit residues: 72.1085 Evaluate side-chains 276 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 ARG Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 68 optimal weight: 0.2980 chunk 188 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 116 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.198458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.157603 restraints weight = 42389.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.153262 restraints weight = 59202.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.147998 restraints weight = 49493.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147880 restraints weight = 48906.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.147929 restraints weight = 45815.525| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24605 Z= 0.118 Angle : 0.545 12.835 33185 Z= 0.281 Chirality : 0.042 0.156 3842 Planarity : 0.004 0.108 4162 Dihedral : 4.736 57.153 3203 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.19 % Favored : 92.64 % Rotamer: Outliers : 3.18 % Allowed : 26.65 % Favored : 70.17 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2963 helix: 1.09 (0.15), residues: 1245 sheet: -0.93 (0.27), residues: 416 loop : -2.00 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 211 TYR 0.017 0.001 TYR G 76 PHE 0.015 0.001 PHE L 148 HIS 0.003 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00289 (24601) covalent geometry : angle 0.54473 (33177) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.74530 ( 8) hydrogen bonds : bond 0.03161 ( 1074) hydrogen bonds : angle 4.28001 ( 3066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 200 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7445 (tp) REVERT: C 101 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: I 52 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (p) REVERT: I 73 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8111 (mm) REVERT: K 172 TYR cc_start: 0.8287 (p90) cc_final: 0.7726 (p90) REVERT: K 177 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8549 (tp) REVERT: K 308 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8392 (mt) REVERT: L 141 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8079 (pp) REVERT: L 211 ARG cc_start: 0.4834 (mmm160) cc_final: 0.4292 (mmm160) REVERT: H 119 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8496 (mt) REVERT: H 291 MET cc_start: 0.7215 (mmm) cc_final: 0.7013 (mmm) REVERT: J 105 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: D 1 MET cc_start: 0.6996 (tpp) cc_final: 0.6774 (tpt) REVERT: D 193 MET cc_start: 0.5095 (mtt) cc_final: 0.4665 (mtt) REVERT: E 208 ASN cc_start: 0.8494 (t0) cc_final: 0.8226 (t0) outliers start: 87 outliers final: 65 residues processed: 269 average time/residue: 0.1584 time to fit residues: 68.0143 Evaluate side-chains 269 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 290 LEU Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 ARG Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 229 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 108 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 143 optimal weight: 0.0050 chunk 136 optimal weight: 20.0000 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.199715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.161611 restraints weight = 42499.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.159481 restraints weight = 56720.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157026 restraints weight = 44872.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.156678 restraints weight = 43958.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155794 restraints weight = 37293.740| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24605 Z= 0.103 Angle : 0.544 12.135 33185 Z= 0.279 Chirality : 0.042 0.165 3842 Planarity : 0.004 0.106 4162 Dihedral : 4.646 57.282 3203 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.15 % Favored : 92.68 % Rotamer: Outliers : 2.63 % Allowed : 27.24 % Favored : 70.14 % 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 aren not related in a simple way. whole: -0.66 (0.16), residues: 2963 helix: 1.22 (0.15), residues: 1245 sheet: -0.89 (0.27), residues: 416 loop : -1.99 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 142 TYR 0.020 0.001 TYR A 181 PHE 0.015 0.001 PHE H 287 HIS 0.003 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00245 (24601) covalent geometry : angle 0.54411 (33177) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.73736 ( 8) hydrogen bonds : bond 0.03012 ( 1074) hydrogen bonds : angle 4.18718 ( 3066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 206 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7506 (tp) REVERT: C 181 TYR cc_start: 0.8757 (p90) cc_final: 0.8151 (p90) REVERT: I 52 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8176 (p) REVERT: I 73 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8107 (mm) REVERT: K 172 TYR cc_start: 0.8262 (p90) cc_final: 0.7692 (p90) REVERT: K 177 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8506 (tp) REVERT: K 287 PHE cc_start: 0.7188 (t80) cc_final: 0.6844 (t80) REVERT: K 291 MET cc_start: 0.7170 (mmm) cc_final: 0.6772 (mmm) REVERT: L 141 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7958 (pp) REVERT: L 211 ARG cc_start: 0.4094 (mmm160) cc_final: 0.3843 (mmm160) REVERT: H 119 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8473 (mt) REVERT: J 105 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5018 (m-80) REVERT: D 193 MET cc_start: 0.5020 (mtt) cc_final: 0.4747 (mtt) REVERT: E 208 ASN cc_start: 0.8312 (t0) cc_final: 0.8094 (t0) REVERT: E 287 PHE cc_start: 0.6858 (t80) cc_final: 0.6467 (t80) REVERT: E 291 MET cc_start: 0.7134 (mmm) cc_final: 0.6646 (mmm) outliers start: 72 outliers final: 57 residues processed: 264 average time/residue: 0.1571 time to fit residues: 66.6622 Evaluate side-chains 263 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 167 ARG Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 158 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN F 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.196697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157913 restraints weight = 42360.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.156176 restraints weight = 60064.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153522 restraints weight = 48047.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152833 restraints weight = 48963.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150841 restraints weight = 45193.701| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24605 Z= 0.165 Angle : 0.586 12.139 33185 Z= 0.300 Chirality : 0.044 0.166 3842 Planarity : 0.004 0.105 4162 Dihedral : 4.700 58.438 3201 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.04 % Rotamer: Outliers : 2.74 % Allowed : 27.02 % Favored : 70.24 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2963 helix: 1.13 (0.15), residues: 1245 sheet: -0.98 (0.27), residues: 416 loop : -2.00 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 142 TYR 0.023 0.001 TYR I 76 PHE 0.024 0.001 PHE E 287 HIS 0.003 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00412 (24601) covalent geometry : angle 0.58573 (33177) SS BOND : bond 0.00028 ( 4) SS BOND : angle 0.70528 ( 8) hydrogen bonds : bond 0.03324 ( 1074) hydrogen bonds : angle 4.29885 ( 3066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5926 Ramachandran restraints generated. 2963 Oldfield, 0 Emsley, 2963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 203 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6165 (tpp80) REVERT: C 73 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7603 (tp) REVERT: I 52 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8403 (p) REVERT: K 172 TYR cc_start: 0.8358 (p90) cc_final: 0.7827 (p90) REVERT: K 177 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8579 (tp) REVERT: K 291 MET cc_start: 0.7182 (mmm) cc_final: 0.6755 (mmm) REVERT: L 141 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8050 (pp) REVERT: H 119 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8526 (mt) REVERT: H 287 PHE cc_start: 0.7146 (t80) cc_final: 0.6732 (t80) REVERT: H 291 MET cc_start: 0.7608 (mmm) cc_final: 0.7000 (mmm) REVERT: J 105 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.4961 (m-80) REVERT: D 1 MET cc_start: 0.6909 (tpp) cc_final: 0.6492 (tpt) REVERT: D 193 MET cc_start: 0.5089 (mtt) cc_final: 0.4772 (mtt) REVERT: E 208 ASN cc_start: 0.8343 (t0) cc_final: 0.8133 (t0) REVERT: E 291 MET cc_start: 0.7119 (mmm) cc_final: 0.6634 (mmm) outliers start: 75 outliers final: 62 residues processed: 264 average time/residue: 0.1548 time to fit residues: 65.2355 Evaluate side-chains 265 residues out of total 2739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 262 TYR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 105 TYR Chi-restraints excluded: chain J residue 167 ARG Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 87 optimal weight: 0.4980 chunk 145 optimal weight: 0.2980 chunk 97 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 153 optimal weight: 0.0570 chunk 230 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.197601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.158503 restraints weight = 42714.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.156024 restraints weight = 58430.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.154463 restraints weight = 50501.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.154128 restraints weight = 46208.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152651 restraints weight = 40424.329| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24605 Z= 0.100 Angle : 0.549 11.305 33185 Z= 0.280 Chirality : 0.043 0.173 3842 Planarity : 0.004 0.103 4162 Dihedral : 4.586 56.915 3201 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 2.37 % Allowed : 27.27 % Favored : 70.35 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2963 helix: 1.25 (0.15), residues: 1245 sheet: -0.89 (0.27), residues: 416 loop : -1.97 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 211 TYR 0.017 0.001 TYR E 262 PHE 0.025 0.001 PHE E 287 HIS 0.003 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00233 (24601) covalent geometry : angle 0.54861 (33177) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.71849 ( 8) hydrogen bonds : bond 0.03012 ( 1074) hydrogen bonds : angle 4.14735 ( 3066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4697.46 seconds wall clock time: 82 minutes 11.10 seconds (4931.10 seconds total)