Starting phenix.real_space_refine on Tue Jun 24 17:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmw_16126/06_2025/8bmw_16126.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 47 5.49 5 S 107 5.16 5 C 18138 2.51 5 N 4786 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28658 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2121 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 258} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1585 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "N" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2029 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain: "R" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 971 Classifications: {'RNA': 48} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 26, 'rna3p_pur': 1, 'rna3p_pyr': 16} Link IDs: {'rna2p': 30, 'rna3p': 17} Chain: "G" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1877 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 1 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2168 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "I" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2164 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6678 Classifications: {'peptide': 829} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 807} Chain: "M" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2383 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Time building chain proxies: 16.81, per 1000 atoms: 0.59 Number of scatterers: 28658 At special positions: 0 Unit cell: (126.566, 119.244, 242.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 47 15.00 O 5580 8.00 N 4786 7.00 C 18138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 223 " - pdb=" SG CYS J 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 75 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 180 " - pdb=" SG CYS L 185 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS H 123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 120 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 275 " distance=2.03 Simple disulfide: pdb=" SG CYS M 220 " - pdb=" SG CYS M 224 " 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: 7.49 Conformation dependent library (CDL) restraints added in 3.7 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 35 sheets defined 44.3% alpha, 12.9% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 10.87 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 80 through 93 removed outlier: 4.634A pdb=" N ASP A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 117 Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.651A pdb=" N VAL A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.649A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 95 through 117 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 95 through 117 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.508A pdb=" N LEU D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 117 Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 80 through 91 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 96 through 117 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.613A pdb=" N VAL E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.714A pdb=" N LEU J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.773A pdb=" N TYR J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 108 Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.597A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 82 Processing helix chain 'L' and resid 144 through 160 removed outlier: 3.697A pdb=" N ARG L 159 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.754A pdb=" N VAL L 183 " --> pdb=" O ILE L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 198 removed outlier: 3.989A pdb=" N ARG L 198 " --> pdb=" O ASN L 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 59 Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.594A pdb=" N GLU N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 84 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 111 through 126 Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 195 through 208 removed outlier: 3.516A pdb=" N GLU N 207 " --> pdb=" O LYS N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 219 removed outlier: 3.571A pdb=" N GLY N 219 " --> pdb=" O LYS N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 252 Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.655A pdb=" N ASN G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'F' and resid 53 through 73 removed outlier: 3.595A pdb=" N ASN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 180 through 200 Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'H' and resid 58 through 77 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.613A pdb=" N LYS H 105 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.612A pdb=" N ALA H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 189 through 205 Processing helix chain 'H' and resid 253 through 270 Proline residue: H 263 - end of helix Processing helix chain 'I' and resid 58 through 77 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.738A pdb=" N ASN I 101 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS I 105 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 120 through 127 Processing helix chain 'I' and resid 189 through 206 Processing helix chain 'I' and resid 253 through 261 Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'K' and resid 17 through 44 removed outlier: 4.477A pdb=" N LYS K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 removed outlier: 3.503A pdb=" N TYR K 62 " --> pdb=" O ILE K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 115 through 136 removed outlier: 3.781A pdb=" N TYR K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 165 removed outlier: 3.710A pdb=" N HIS K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 211 through 224 Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 271 through 283 Processing helix chain 'K' and resid 283 through 300 Processing helix chain 'K' and resid 323 through 329 Processing helix chain 'K' and resid 332 through 364 removed outlier: 3.982A pdb=" N TYR K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER K 351 " --> pdb=" O THR K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 removed outlier: 3.791A pdb=" N LEU K 374 " --> pdb=" O ALA K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 408 Processing helix chain 'K' and resid 430 through 441 Processing helix chain 'K' and resid 442 through 446 removed outlier: 4.096A pdb=" N TYR K 446 " --> pdb=" O SER K 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 442 through 446' Processing helix chain 'K' and resid 482 through 495 removed outlier: 4.512A pdb=" N ASN K 494 " --> pdb=" O ASP K 490 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 502 Processing helix chain 'K' and resid 516 through 521 Processing helix chain 'K' and resid 534 through 541 Processing helix chain 'K' and resid 560 through 567 Processing helix chain 'K' and resid 570 through 598 Processing helix chain 'K' and resid 602 through 616 Processing helix chain 'K' and resid 633 through 643 Processing helix chain 'K' and resid 644 through 649 Processing helix chain 'K' and resid 665 through 680 Processing helix chain 'K' and resid 701 through 712 Processing helix chain 'K' and resid 726 through 736 Processing helix chain 'K' and resid 740 through 750 removed outlier: 3.638A pdb=" N ASN K 750 " --> pdb=" O GLU K 746 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 775 removed outlier: 4.436A pdb=" N LYS K 756 " --> pdb=" O GLU K 752 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER K 764 " --> pdb=" O ASP K 760 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU K 765 " --> pdb=" O LYS K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 776 through 790 Processing helix chain 'K' and resid 795 through 806 removed outlier: 3.872A pdb=" N ARG K 799 " --> pdb=" O SER K 795 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 829 removed outlier: 3.783A pdb=" N ILE K 825 " --> pdb=" O ILE K 821 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 829 " --> pdb=" O ILE K 825 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 47 Processing helix chain 'M' and resid 86 through 91 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 179 through 185 removed outlier: 4.057A pdb=" N ASP M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.689A pdb=" N ILE M 299 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 19 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 37 through 40 removed outlier: 4.693A pdb=" N LYS J 40 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'L' and resid 91 through 95 Processing sheet with id=AA6, first strand: chain 'L' and resid 102 through 107 Processing sheet with id=AA7, first strand: chain 'N' and resid 142 through 144 Processing sheet with id=AA8, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.479A pdb=" N ASP G 219 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG G 20 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU G 217 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU G 22 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE G 215 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 236 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'G' and resid 132 through 137 Processing sheet with id=AB4, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.575A pdb=" N LYS F 18 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP F 219 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 20 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU F 217 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 236 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'F' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.532A pdb=" N LEU F 155 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AC1, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'H' and resid 147 through 152 removed outlier: 3.671A pdb=" N VAL H 168 " --> pdb=" O MET H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 135 through 137 removed outlier: 3.559A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 135 through 137 removed outlier: 4.307A pdb=" N LYS I 225 " --> pdb=" O ASP I 21 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU I 23 " --> pdb=" O PHE I 223 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE I 223 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 147 through 151 Processing sheet with id=AC6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'K' and resid 382 through 387 removed outlier: 6.692A pdb=" N ALA K 311 " --> pdb=" O TYR K 424 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR K 424 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY K 313 " --> pdb=" O PHE K 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP K 319 " --> pdb=" O ASP K 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 447 through 448 removed outlier: 4.090A pdb=" N ILE M 239 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE M 234 " --> pdb=" O PHE M 276 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 276 " --> pdb=" O PHE M 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA M 236 " --> pdb=" O GLU M 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU M 274 " --> pdb=" O ALA M 236 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR M 238 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 271 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 273 " --> pdb=" O GLY M 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 505 through 507 Processing sheet with id=AD1, first strand: chain 'K' and resid 625 through 627 removed outlier: 3.697A pdb=" N ASN K 724 " --> pdb=" O ILE K 690 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 717 through 718 Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.551A pdb=" N GLY M 10 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET M 160 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA M 148 " --> pdb=" O MET M 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS M 140 " --> pdb=" O GLU M 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.378A pdb=" N LYS M 133 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 227 through 228 Processing sheet with id=AD7, first strand: chain 'M' and resid 243 through 244 Processing sheet with id=AD8, first strand: chain 'M' and resid 247 through 249 removed outlier: 6.196A pdb=" N GLY M 248 " --> pdb=" O LYS M 259 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 9.64 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4873 1.32 - 1.45: 7460 1.45 - 1.57: 16633 1.57 - 1.69: 94 1.69 - 1.81: 177 Bond restraints: 29237 Sorted by residual: bond pdb=" N ILE I 57 " pdb=" CA ILE I 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" CA SER J 163 " pdb=" CB SER J 163 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.38e-02 5.25e+03 1.98e+01 bond pdb=" CA SER I 60 " pdb=" CB SER I 60 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.56e-02 4.11e+03 1.11e+01 bond pdb=" CA SER H 83 " pdb=" CB SER H 83 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.65e-02 3.67e+03 1.07e+01 bond pdb=" CA SER I 61 " pdb=" CB SER I 61 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 ... (remaining 29232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 38868 1.66 - 3.31: 599 3.31 - 4.97: 96 4.97 - 6.63: 22 6.63 - 8.28: 8 Bond angle restraints: 39593 Sorted by residual: angle pdb=" N SER L 24 " pdb=" CA SER L 24 " pdb=" C SER L 24 " ideal model delta sigma weight residual 114.62 106.54 8.08 1.14e+00 7.69e-01 5.02e+01 angle pdb=" N ARG J 164 " pdb=" CA ARG J 164 " pdb=" C ARG J 164 " ideal model delta sigma weight residual 113.19 104.91 8.28 1.19e+00 7.06e-01 4.84e+01 angle pdb=" C PRO H 189 " pdb=" CA PRO H 189 " pdb=" CB PRO H 189 " ideal model delta sigma weight residual 111.23 103.69 7.54 1.28e+00 6.10e-01 3.47e+01 angle pdb=" C TYR K 282 " pdb=" CA TYR K 282 " pdb=" CB TYR K 282 " ideal model delta sigma weight residual 109.07 117.25 -8.18 1.68e+00 3.54e-01 2.37e+01 angle pdb=" N LEU I 112 " pdb=" CA LEU I 112 " pdb=" C LEU I 112 " ideal model delta sigma weight residual 111.07 105.90 5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 39588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 17724 35.71 - 71.42: 263 71.42 - 107.14: 9 107.14 - 142.85: 0 142.85 - 178.56: 11 Dihedral angle restraints: 18007 sinusoidal: 7890 harmonic: 10117 Sorted by residual: dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 120 " pdb=" CB CYS H 120 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" O4' U R 23 " pdb=" C1' U R 23 " pdb=" N1 U R 23 " pdb=" C2 U R 23 " ideal model delta sinusoidal sigma weight residual 200.00 28.17 171.83 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CB CYS L 75 " pdb=" SG CYS L 75 " pdb=" SG CYS L 78 " pdb=" CB CYS L 78 " ideal model delta sinusoidal sigma weight residual 93.00 9.89 83.11 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 18004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3706 0.050 - 0.099: 648 0.099 - 0.149: 146 0.149 - 0.198: 14 0.198 - 0.248: 10 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ARG J 164 " pdb=" N ARG J 164 " pdb=" C ARG J 164 " pdb=" CB ARG J 164 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO H 189 " pdb=" N PRO H 189 " pdb=" C PRO H 189 " pdb=" CB PRO H 189 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE I 114 " pdb=" N ILE I 114 " pdb=" C ILE I 114 " pdb=" CB ILE I 114 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 4521 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 88 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ASP H 88 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP H 88 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR H 89 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 82 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C CYS H 82 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS H 82 " -0.017 2.00e-02 2.50e+03 pdb=" N SER H 83 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 115 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C PHE I 115 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE I 115 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP I 116 " -0.012 2.00e-02 2.50e+03 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2440 2.74 - 3.28: 30904 3.28 - 3.82: 49718 3.82 - 4.36: 57607 4.36 - 4.90: 98284 Nonbonded interactions: 238953 Sorted by model distance: nonbonded pdb=" OG1 THR L 38 " pdb=" OP1 U R 9 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR K 173 " pdb=" OD1 ASN K 213 " model vdw 2.198 3.040 nonbonded pdb=" O2' U R 23 " pdb=" O PHE G 113 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP L 94 " pdb=" OG1 THR L 137 " model vdw 2.201 3.040 nonbonded pdb=" O LEU L 151 " pdb=" OG SER L 154 " model vdw 2.201 3.040 ... (remaining 238948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 137) selection = chain 'B' selection = (chain 'C' and resid 19 through 137) selection = (chain 'D' and resid 19 through 137) selection = (chain 'E' and resid 19 through 137) } ncs_group { reference = (chain 'F' and resid 4 through 244) selection = (chain 'G' and (resid 4 through 94 or resid 101 through 244)) } ncs_group { reference = (chain 'H' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 121 through 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 278)) selection = chain 'I' } 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 69.670 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.130 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.003 0.061 29252 Z= 0.185 Angle : 0.539 8.282 39623 Z= 0.331 Chirality : 0.042 0.248 4524 Planarity : 0.003 0.043 4852 Dihedral : 12.902 178.559 11466 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 0.49 % Allowed : 11.33 % Favored : 88.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3441 helix: 2.45 (0.14), residues: 1468 sheet: 0.20 (0.25), residues: 449 loop : -1.57 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 249 HIS 0.004 0.001 HIS K 225 PHE 0.014 0.001 PHE G 144 TYR 0.016 0.001 TYR H 195 ARG 0.008 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.15673 ( 1274) hydrogen bonds : angle 6.62998 ( 3747) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.98010 ( 30) covalent geometry : bond 0.00317 (29237) covalent geometry : angle 0.53678 (39593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 865 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.9424 (tp) cc_final: 0.9158 (tt) REVERT: A 56 PHE cc_start: 0.8841 (t80) cc_final: 0.8597 (t80) REVERT: A 60 ARG cc_start: 0.9199 (mmp80) cc_final: 0.8853 (mmm160) REVERT: A 79 ILE cc_start: 0.8988 (mm) cc_final: 0.8661 (mp) REVERT: A 111 ASP cc_start: 0.8846 (t0) cc_final: 0.8515 (t0) REVERT: A 131 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8954 (mt-10) REVERT: B 22 ASP cc_start: 0.8657 (m-30) cc_final: 0.8037 (m-30) REVERT: B 39 ASN cc_start: 0.8836 (p0) cc_final: 0.8418 (p0) REVERT: B 90 SER cc_start: 0.9627 (m) cc_final: 0.9219 (p) REVERT: B 98 ASP cc_start: 0.8796 (t70) cc_final: 0.8531 (t0) REVERT: B 103 LEU cc_start: 0.9725 (mt) cc_final: 0.9347 (mt) REVERT: B 107 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9511 (pttt) REVERT: B 127 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8507 (mmtt) REVERT: B 128 THR cc_start: 0.9064 (p) cc_final: 0.8629 (t) REVERT: B 129 PHE cc_start: 0.9154 (t80) cc_final: 0.8922 (t80) REVERT: B 134 ASN cc_start: 0.9070 (m110) cc_final: 0.8702 (m110) REVERT: C 22 ASP cc_start: 0.8708 (m-30) cc_final: 0.8411 (m-30) REVERT: C 44 TYR cc_start: 0.8761 (t80) cc_final: 0.8483 (t80) REVERT: C 58 GLN cc_start: 0.9647 (mm-40) cc_final: 0.9245 (mm-40) REVERT: C 71 MET cc_start: 0.9365 (mtm) cc_final: 0.9056 (mtm) REVERT: C 92 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9182 (ttmm) REVERT: C 97 LYS cc_start: 0.9659 (ptpt) cc_final: 0.9424 (pptt) REVERT: C 101 ASN cc_start: 0.9526 (m-40) cc_final: 0.9325 (m-40) REVERT: C 114 THR cc_start: 0.9425 (m) cc_final: 0.9013 (p) REVERT: D 44 TYR cc_start: 0.9288 (t80) cc_final: 0.8748 (t80) REVERT: D 58 GLN cc_start: 0.9420 (mp10) cc_final: 0.9132 (mm-40) REVERT: D 90 SER cc_start: 0.9500 (m) cc_final: 0.9243 (p) REVERT: D 114 THR cc_start: 0.9520 (m) cc_final: 0.9174 (p) REVERT: D 127 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8948 (mtpt) REVERT: D 131 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8831 (mt-10) REVERT: E 55 SER cc_start: 0.9756 (m) cc_final: 0.9481 (p) REVERT: E 76 ARG cc_start: 0.9417 (mmm-85) cc_final: 0.8997 (mmm-85) REVERT: E 78 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 82 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8945 (tm-30) REVERT: E 101 ASN cc_start: 0.9396 (m110) cc_final: 0.8799 (m110) REVERT: E 105 TYR cc_start: 0.9073 (m-10) cc_final: 0.8464 (m-80) REVERT: E 114 THR cc_start: 0.9441 (m) cc_final: 0.9175 (p) REVERT: E 131 GLU cc_start: 0.8986 (tp30) cc_final: 0.8650 (tm-30) REVERT: E 135 ILE cc_start: 0.9508 (mm) cc_final: 0.9151 (mm) REVERT: J 46 MET cc_start: 0.8427 (mtp) cc_final: 0.7621 (mtp) REVERT: J 81 LEU cc_start: 0.9348 (mt) cc_final: 0.9066 (mp) REVERT: J 146 PHE cc_start: 0.9023 (m-80) cc_final: 0.8750 (m-80) REVERT: J 166 SER cc_start: 0.8525 (m) cc_final: 0.8212 (t) REVERT: J 209 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8605 (mp0) REVERT: J 229 MET cc_start: 0.8142 (mtp) cc_final: 0.7610 (ttm) REVERT: L 8 MET cc_start: 0.8810 (tmm) cc_final: 0.8345 (tmm) REVERT: L 40 LYS cc_start: 0.9236 (tttt) cc_final: 0.8900 (tttm) REVERT: L 62 GLU cc_start: 0.8949 (tp30) cc_final: 0.8593 (tp30) REVERT: L 64 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8384 (tm-30) REVERT: L 79 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8988 (mttp) REVERT: L 115 GLN cc_start: 0.8786 (mm110) cc_final: 0.8363 (mm-40) REVERT: L 118 LYS cc_start: 0.9531 (tppp) cc_final: 0.9071 (tppt) REVERT: L 126 GLN cc_start: 0.8242 (tt0) cc_final: 0.8037 (tt0) REVERT: L 178 GLU cc_start: 0.8656 (pt0) cc_final: 0.8322 (pt0) REVERT: N 30 ARG cc_start: 0.9015 (mmp-170) cc_final: 0.8663 (mmm-85) REVERT: N 49 MET cc_start: 0.9541 (tmm) cc_final: 0.9264 (tmm) REVERT: N 102 GLN cc_start: 0.9163 (tp40) cc_final: 0.8673 (tp40) REVERT: N 196 GLU cc_start: 0.8377 (tp30) cc_final: 0.7703 (tp30) REVERT: N 232 TYR cc_start: 0.9002 (p90) cc_final: 0.8576 (p90) REVERT: N 249 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8925 (ptm-80) REVERT: G 40 ASP cc_start: 0.9099 (m-30) cc_final: 0.8880 (p0) REVERT: G 52 ILE cc_start: 0.9686 (mt) cc_final: 0.9373 (tp) REVERT: G 66 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8989 (mt-10) REVERT: G 137 MET cc_start: 0.8758 (mpp) cc_final: 0.8457 (mpp) REVERT: G 168 MET cc_start: 0.9030 (ttp) cc_final: 0.8604 (ttm) REVERT: G 169 MET cc_start: 0.8556 (mmm) cc_final: 0.8277 (mmm) REVERT: F 33 GLN cc_start: 0.9223 (mp10) cc_final: 0.8899 (mp10) REVERT: F 43 ILE cc_start: 0.8091 (pt) cc_final: 0.7409 (pt) REVERT: F 62 ARG cc_start: 0.9428 (ttt90) cc_final: 0.9124 (ttm-80) REVERT: F 73 ASN cc_start: 0.9403 (t0) cc_final: 0.9138 (t0) REVERT: F 121 TYR cc_start: 0.8643 (m-80) cc_final: 0.8402 (m-80) REVERT: F 135 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8196 (ttm170) REVERT: F 157 TYR cc_start: 0.6195 (m-80) cc_final: 0.5358 (m-80) REVERT: F 174 ASN cc_start: 0.9104 (m-40) cc_final: 0.7265 (m-40) REVERT: F 239 LYS cc_start: 0.9639 (mmtm) cc_final: 0.8966 (mmmm) REVERT: H 56 ILE cc_start: 0.9394 (pt) cc_final: 0.9151 (mm) REVERT: H 145 TYR cc_start: 0.8610 (p90) cc_final: 0.7706 (p90) REVERT: H 174 ASP cc_start: 0.8597 (t0) cc_final: 0.7946 (t70) REVERT: H 238 ASP cc_start: 0.8961 (p0) cc_final: 0.8754 (p0) REVERT: H 255 ASP cc_start: 0.9039 (m-30) cc_final: 0.8602 (p0) REVERT: H 261 MET cc_start: 0.9572 (mmp) cc_final: 0.9299 (mmm) REVERT: H 265 MET cc_start: 0.9422 (mtp) cc_final: 0.9124 (mtt) REVERT: H 266 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9204 (mt-10) REVERT: H 270 ASN cc_start: 0.9282 (m110) cc_final: 0.9070 (m110) REVERT: I 17 MET cc_start: 0.8692 (tpp) cc_final: 0.8193 (tpp) REVERT: I 99 ASP cc_start: 0.9488 (m-30) cc_final: 0.9252 (p0) REVERT: I 110 GLN cc_start: 0.9554 (tp40) cc_final: 0.9291 (tp-100) REVERT: I 118 TYR cc_start: 0.9097 (m-80) cc_final: 0.8837 (m-10) REVERT: I 261 MET cc_start: 0.9599 (mmm) cc_final: 0.9296 (mpp) REVERT: I 275 TYR cc_start: 0.8871 (p90) cc_final: 0.8376 (p90) REVERT: K 56 ASP cc_start: 0.9163 (m-30) cc_final: 0.8864 (m-30) REVERT: K 60 MET cc_start: 0.9403 (tmm) cc_final: 0.8868 (tmm) REVERT: K 61 ILE cc_start: 0.9285 (mt) cc_final: 0.8903 (mt) REVERT: K 81 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8556 (mt-10) REVERT: K 128 ARG cc_start: 0.9504 (ttm110) cc_final: 0.9063 (ptp-110) REVERT: K 129 LYS cc_start: 0.9618 (mttt) cc_final: 0.9351 (mtmt) REVERT: K 156 LEU cc_start: 0.9004 (mt) cc_final: 0.8740 (mt) REVERT: K 201 ASP cc_start: 0.9284 (t0) cc_final: 0.8718 (t0) REVERT: K 202 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8261 (pt0) REVERT: K 314 TYR cc_start: 0.8720 (m-80) cc_final: 0.8267 (m-80) REVERT: K 330 PHE cc_start: 0.9054 (m-80) cc_final: 0.8228 (m-80) REVERT: K 336 MET cc_start: 0.8793 (mmm) cc_final: 0.8422 (mmm) REVERT: K 369 ILE cc_start: 0.9443 (mt) cc_final: 0.9062 (mm) REVERT: K 406 SER cc_start: 0.9202 (m) cc_final: 0.8947 (p) REVERT: K 474 ARG cc_start: 0.3068 (mtt180) cc_final: 0.2602 (mtt180) REVERT: K 481 LEU cc_start: 0.8464 (tp) cc_final: 0.8169 (tp) REVERT: K 520 ASP cc_start: 0.7929 (m-30) cc_final: 0.7635 (m-30) REVERT: K 538 ILE cc_start: 0.9469 (mt) cc_final: 0.9215 (mt) REVERT: K 587 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8441 (tppt) REVERT: K 597 MET cc_start: 0.9059 (mmt) cc_final: 0.8845 (mmm) REVERT: K 625 ILE cc_start: 0.9407 (mt) cc_final: 0.9091 (mm) REVERT: K 639 VAL cc_start: 0.9644 (t) cc_final: 0.9433 (p) REVERT: K 641 MET cc_start: 0.9271 (ttt) cc_final: 0.8968 (ttm) REVERT: K 677 MET cc_start: 0.9127 (ttp) cc_final: 0.8867 (ttp) REVERT: K 692 VAL cc_start: 0.9476 (t) cc_final: 0.9269 (p) REVERT: K 730 GLU cc_start: 0.8995 (tt0) cc_final: 0.8744 (tp30) REVERT: K 739 ASP cc_start: 0.8448 (p0) cc_final: 0.8248 (p0) REVERT: M 16 MET cc_start: 0.8711 (mmt) cc_final: 0.8352 (mmp) REVERT: M 28 ASN cc_start: 0.9056 (t0) cc_final: 0.8854 (t0) REVERT: M 62 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9341 (mm) REVERT: M 69 TYR cc_start: 0.8126 (t80) cc_final: 0.7061 (t80) REVERT: M 82 ILE cc_start: 0.9314 (pt) cc_final: 0.8830 (mm) REVERT: M 144 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8309 (mm110) REVERT: M 169 PHE cc_start: 0.9169 (m-80) cc_final: 0.8955 (m-10) REVERT: M 215 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8968 (tttm) REVERT: M 231 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8861 (mmtp) outliers start: 15 outliers final: 4 residues processed: 876 average time/residue: 0.4681 time to fit residues: 621.7073 Evaluate side-chains 554 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 549 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 145 optimal weight: 0.2980 chunk 89 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 104 optimal weight: 0.0070 chunk 164 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 314 optimal weight: 0.5980 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN D 73 GLN E 39 ASN J 148 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 141 ASN K 155 GLN K 181 HIS K 223 GLN M 46 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045475 restraints weight = 141832.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047269 restraints weight = 74084.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.048494 restraints weight = 46761.022| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29252 Z= 0.144 Angle : 0.659 12.190 39623 Z= 0.342 Chirality : 0.044 0.228 4524 Planarity : 0.004 0.054 4852 Dihedral : 13.250 178.175 4577 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 17.86 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3441 helix: 2.03 (0.14), residues: 1466 sheet: 0.09 (0.25), residues: 433 loop : -1.65 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 108 HIS 0.004 0.001 HIS M 113 PHE 0.031 0.001 PHE K 245 TYR 0.021 0.002 TYR L 104 ARG 0.014 0.001 ARG K 786 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 1274) hydrogen bonds : angle 5.29698 ( 3747) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.87983 ( 30) covalent geometry : bond 0.00315 (29237) covalent geometry : angle 0.65723 (39593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 656 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8642 (m-30) cc_final: 0.8162 (t0) REVERT: A 29 ILE cc_start: 0.9410 (tp) cc_final: 0.9070 (tt) REVERT: A 42 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 56 PHE cc_start: 0.8925 (t80) cc_final: 0.8520 (t80) REVERT: A 60 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8874 (mmm160) REVERT: A 79 ILE cc_start: 0.8915 (mm) cc_final: 0.8629 (mp) REVERT: A 110 TYR cc_start: 0.9034 (t80) cc_final: 0.8731 (t80) REVERT: A 111 ASP cc_start: 0.9029 (t0) cc_final: 0.8730 (t0) REVERT: A 131 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9030 (mt-10) REVERT: B 22 ASP cc_start: 0.8870 (m-30) cc_final: 0.8020 (m-30) REVERT: B 26 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8409 (ptp90) REVERT: B 44 TYR cc_start: 0.9345 (t80) cc_final: 0.9000 (t80) REVERT: B 56 PHE cc_start: 0.9426 (t80) cc_final: 0.9110 (t80) REVERT: B 69 TYR cc_start: 0.9124 (t80) cc_final: 0.8770 (t80) REVERT: B 73 GLN cc_start: 0.9304 (tp40) cc_final: 0.8971 (mp10) REVERT: B 78 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8864 (tp30) REVERT: B 90 SER cc_start: 0.9616 (m) cc_final: 0.9202 (p) REVERT: B 103 LEU cc_start: 0.9779 (mt) cc_final: 0.9452 (tp) REVERT: B 128 THR cc_start: 0.9355 (p) cc_final: 0.8460 (p) REVERT: B 129 PHE cc_start: 0.9270 (t80) cc_final: 0.9012 (t80) REVERT: B 131 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8733 (mt-10) REVERT: B 134 ASN cc_start: 0.9209 (m-40) cc_final: 0.8845 (m110) REVERT: C 22 ASP cc_start: 0.9071 (m-30) cc_final: 0.8713 (m-30) REVERT: C 45 VAL cc_start: 0.9341 (t) cc_final: 0.9013 (p) REVERT: C 71 MET cc_start: 0.9429 (mtm) cc_final: 0.9049 (mtm) REVERT: C 77 ASP cc_start: 0.9059 (t0) cc_final: 0.8840 (t0) REVERT: C 80 ASP cc_start: 0.8747 (t70) cc_final: 0.8509 (t70) REVERT: C 105 TYR cc_start: 0.9355 (m-80) cc_final: 0.9137 (m-80) REVERT: C 134 ASN cc_start: 0.9683 (m-40) cc_final: 0.9417 (m110) REVERT: D 44 TYR cc_start: 0.9169 (t80) cc_final: 0.8733 (t80) REVERT: D 58 GLN cc_start: 0.9487 (mp10) cc_final: 0.9191 (mm-40) REVERT: D 90 SER cc_start: 0.9443 (m) cc_final: 0.9232 (p) REVERT: D 101 ASN cc_start: 0.9562 (m110) cc_final: 0.9346 (m110) REVERT: D 131 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8878 (mt-10) REVERT: E 42 GLU cc_start: 0.8573 (pt0) cc_final: 0.8304 (pm20) REVERT: E 48 SER cc_start: 0.9757 (m) cc_final: 0.9529 (p) REVERT: E 55 SER cc_start: 0.9766 (m) cc_final: 0.9479 (p) REVERT: E 82 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9025 (tm-30) REVERT: E 101 ASN cc_start: 0.9482 (m110) cc_final: 0.8969 (m110) REVERT: E 105 TYR cc_start: 0.9311 (m-10) cc_final: 0.8705 (m-80) REVERT: E 114 THR cc_start: 0.9472 (m) cc_final: 0.9215 (p) REVERT: E 130 LYS cc_start: 0.9522 (ptmt) cc_final: 0.9238 (ttpp) REVERT: E 131 GLU cc_start: 0.9088 (tp30) cc_final: 0.8611 (tm-30) REVERT: E 134 ASN cc_start: 0.9450 (m-40) cc_final: 0.8707 (m-40) REVERT: E 135 ILE cc_start: 0.9591 (mm) cc_final: 0.9229 (mm) REVERT: J 6 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8238 (tp) REVERT: J 44 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7656 (pp20) REVERT: J 46 MET cc_start: 0.8378 (mtp) cc_final: 0.7764 (mtp) REVERT: J 56 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.8480 (m) REVERT: J 81 LEU cc_start: 0.9378 (mt) cc_final: 0.9176 (mp) REVERT: J 105 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8309 (mt-10) REVERT: J 146 PHE cc_start: 0.9191 (m-80) cc_final: 0.8879 (m-80) REVERT: J 148 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9122 (mm-40) REVERT: J 166 SER cc_start: 0.9066 (m) cc_final: 0.8654 (t) REVERT: J 209 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8398 (mp0) REVERT: J 229 MET cc_start: 0.8562 (mtp) cc_final: 0.8322 (mtp) REVERT: L 62 GLU cc_start: 0.8871 (tp30) cc_final: 0.8172 (mp0) REVERT: L 113 LYS cc_start: 0.9405 (ttmm) cc_final: 0.9106 (tppt) REVERT: L 115 GLN cc_start: 0.8849 (mm110) cc_final: 0.8519 (mm-40) REVERT: L 118 LYS cc_start: 0.9380 (tppp) cc_final: 0.9166 (tppt) REVERT: L 127 ILE cc_start: 0.9519 (pt) cc_final: 0.9020 (mm) REVERT: L 178 GLU cc_start: 0.9119 (pt0) cc_final: 0.8862 (pm20) REVERT: L 199 TYR cc_start: 0.8784 (m-10) cc_final: 0.8416 (m-10) REVERT: N 49 MET cc_start: 0.9593 (tmm) cc_final: 0.9283 (tmm) REVERT: N 72 VAL cc_start: 0.8789 (t) cc_final: 0.8423 (p) REVERT: N 155 MET cc_start: 0.8883 (pmm) cc_final: 0.8677 (pmm) REVERT: N 161 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8807 (p) REVERT: N 196 GLU cc_start: 0.8419 (tp30) cc_final: 0.7717 (tp30) REVERT: N 229 GLU cc_start: 0.8216 (tp30) cc_final: 0.7863 (tp30) REVERT: G 40 ASP cc_start: 0.9199 (m-30) cc_final: 0.8909 (p0) REVERT: G 66 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9050 (mt-10) REVERT: G 156 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: G 167 MET cc_start: 0.7793 (tpp) cc_final: 0.7451 (tpp) REVERT: G 168 MET cc_start: 0.8804 (ttp) cc_final: 0.8592 (ttm) REVERT: F 33 GLN cc_start: 0.9291 (mp10) cc_final: 0.8930 (mp10) REVERT: F 73 ASN cc_start: 0.9486 (t0) cc_final: 0.9199 (t0) REVERT: F 121 TYR cc_start: 0.8791 (m-80) cc_final: 0.8500 (m-80) REVERT: F 137 MET cc_start: 0.8269 (ptp) cc_final: 0.7973 (ptp) REVERT: F 168 MET cc_start: 0.9031 (ttp) cc_final: 0.8823 (ttp) REVERT: F 169 MET cc_start: 0.8975 (mtp) cc_final: 0.8737 (mtp) REVERT: F 239 LYS cc_start: 0.9470 (mmtm) cc_final: 0.9269 (mmmm) REVERT: H 56 ILE cc_start: 0.9393 (pt) cc_final: 0.9076 (mm) REVERT: H 110 GLN cc_start: 0.9611 (tp40) cc_final: 0.9205 (mp10) REVERT: H 145 TYR cc_start: 0.8161 (p90) cc_final: 0.7711 (p90) REVERT: H 174 ASP cc_start: 0.8626 (t0) cc_final: 0.8170 (t70) REVERT: H 182 LYS cc_start: 0.9270 (ttmt) cc_final: 0.9064 (tttm) REVERT: H 193 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9138 (pt) REVERT: H 200 MET cc_start: 0.9189 (tpp) cc_final: 0.8752 (tmm) REVERT: H 255 ASP cc_start: 0.9156 (m-30) cc_final: 0.8691 (p0) REVERT: H 261 MET cc_start: 0.9589 (mmp) cc_final: 0.9257 (mmm) REVERT: H 265 MET cc_start: 0.9547 (mtp) cc_final: 0.9232 (mtt) REVERT: H 266 GLU cc_start: 0.9523 (mt-10) cc_final: 0.9218 (mt-10) REVERT: I 99 ASP cc_start: 0.9498 (m-30) cc_final: 0.9227 (p0) REVERT: I 110 GLN cc_start: 0.9632 (tp40) cc_final: 0.9343 (tp-100) REVERT: I 118 TYR cc_start: 0.9038 (m-80) cc_final: 0.8731 (m-10) REVERT: I 129 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8988 (mmm) REVERT: I 152 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7447 (mmm) REVERT: I 182 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7934 (tptp) REVERT: I 183 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: K 56 ASP cc_start: 0.9090 (m-30) cc_final: 0.8785 (m-30) REVERT: K 60 MET cc_start: 0.9207 (tmm) cc_final: 0.8791 (tmm) REVERT: K 61 ILE cc_start: 0.9180 (mt) cc_final: 0.8739 (mt) REVERT: K 128 ARG cc_start: 0.9527 (ttm110) cc_final: 0.9206 (ptp-110) REVERT: K 160 LEU cc_start: 0.9448 (mm) cc_final: 0.9178 (mt) REVERT: K 270 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (t) REVERT: K 273 LYS cc_start: 0.9501 (tppt) cc_final: 0.8920 (mttm) REVERT: K 274 GLU cc_start: 0.8568 (mp0) cc_final: 0.8037 (mp0) REVERT: K 314 TYR cc_start: 0.8613 (m-80) cc_final: 0.8108 (m-80) REVERT: K 330 PHE cc_start: 0.9092 (m-80) cc_final: 0.8428 (m-80) REVERT: K 336 MET cc_start: 0.8877 (mmm) cc_final: 0.8426 (mmm) REVERT: K 369 ILE cc_start: 0.9373 (mt) cc_final: 0.8948 (mm) REVERT: K 386 VAL cc_start: 0.9115 (m) cc_final: 0.8873 (m) REVERT: K 406 SER cc_start: 0.9197 (m) cc_final: 0.8958 (p) REVERT: K 435 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8269 (t80) REVERT: K 438 MET cc_start: 0.8646 (mmt) cc_final: 0.8307 (mmt) REVERT: K 474 ARG cc_start: 0.2932 (mtt180) cc_final: 0.2450 (mtt180) REVERT: K 481 LEU cc_start: 0.8588 (tp) cc_final: 0.8269 (tp) REVERT: K 520 ASP cc_start: 0.8003 (m-30) cc_final: 0.7727 (m-30) REVERT: K 527 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8796 (mmtt) REVERT: K 619 TYR cc_start: 0.8787 (p90) cc_final: 0.8538 (p90) REVERT: K 625 ILE cc_start: 0.9456 (mt) cc_final: 0.9132 (mm) REVERT: K 641 MET cc_start: 0.9409 (ttt) cc_final: 0.9207 (ttm) REVERT: K 667 GLN cc_start: 0.9098 (pm20) cc_final: 0.8762 (pm20) REVERT: K 677 MET cc_start: 0.8915 (ttp) cc_final: 0.8539 (ttp) REVERT: M 16 MET cc_start: 0.8712 (mmt) cc_final: 0.8286 (mmp) REVERT: M 40 LEU cc_start: 0.9490 (mm) cc_final: 0.9272 (mt) REVERT: M 82 ILE cc_start: 0.9298 (pt) cc_final: 0.8949 (tt) REVERT: M 144 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8353 (mm110) REVERT: M 231 LYS cc_start: 0.9242 (mmtt) cc_final: 0.9021 (mmmt) outliers start: 84 outliers final: 25 residues processed: 711 average time/residue: 0.3942 time to fit residues: 448.4452 Evaluate side-chains 582 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 545 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 148 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 259 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 HIS G 21 ASN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 734 ASN ** M 144 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.054758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046263 restraints weight = 140944.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048036 restraints weight = 72657.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049266 restraints weight = 45477.896| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29252 Z= 0.138 Angle : 0.634 10.585 39623 Z= 0.328 Chirality : 0.044 0.359 4524 Planarity : 0.004 0.049 4852 Dihedral : 13.146 179.258 4571 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 18.19 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3441 helix: 1.84 (0.14), residues: 1465 sheet: 0.06 (0.24), residues: 447 loop : -1.67 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 182 HIS 0.002 0.001 HIS K 775 PHE 0.035 0.001 PHE E 56 TYR 0.020 0.001 TYR F 212 ARG 0.008 0.000 ARG G 47 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1274) hydrogen bonds : angle 5.08124 ( 3747) SS BOND : bond 0.00612 ( 15) SS BOND : angle 1.76379 ( 30) covalent geometry : bond 0.00306 (29237) covalent geometry : angle 0.63279 (39593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 585 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8712 (m-30) cc_final: 0.8229 (t0) REVERT: A 29 ILE cc_start: 0.9393 (tp) cc_final: 0.9160 (tp) REVERT: A 42 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7833 (mm-30) REVERT: A 56 PHE cc_start: 0.8947 (t80) cc_final: 0.8578 (t80) REVERT: A 60 ARG cc_start: 0.9275 (mmp80) cc_final: 0.8882 (mmm160) REVERT: A 79 ILE cc_start: 0.8937 (mm) cc_final: 0.8657 (mp) REVERT: A 110 TYR cc_start: 0.9033 (t80) cc_final: 0.8790 (t80) REVERT: A 111 ASP cc_start: 0.9002 (t0) cc_final: 0.8727 (t70) REVERT: A 131 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9010 (mt-10) REVERT: B 22 ASP cc_start: 0.8925 (m-30) cc_final: 0.8216 (m-30) REVERT: B 26 ARG cc_start: 0.9144 (ptp-110) cc_final: 0.8493 (ptp90) REVERT: B 44 TYR cc_start: 0.9331 (t80) cc_final: 0.8940 (t80) REVERT: B 78 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8501 (mm-30) REVERT: B 90 SER cc_start: 0.9615 (m) cc_final: 0.9217 (p) REVERT: B 103 LEU cc_start: 0.9767 (mt) cc_final: 0.9458 (tp) REVERT: B 128 THR cc_start: 0.9368 (p) cc_final: 0.8461 (p) REVERT: B 129 PHE cc_start: 0.9196 (t80) cc_final: 0.8935 (t80) REVERT: B 131 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8775 (mt-10) REVERT: B 134 ASN cc_start: 0.9181 (m-40) cc_final: 0.8793 (m110) REVERT: C 22 ASP cc_start: 0.9206 (m-30) cc_final: 0.8928 (m-30) REVERT: C 44 TYR cc_start: 0.9076 (t80) cc_final: 0.8707 (t80) REVERT: C 45 VAL cc_start: 0.9248 (t) cc_final: 0.8935 (p) REVERT: C 71 MET cc_start: 0.9400 (mtm) cc_final: 0.9010 (mtm) REVERT: C 77 ASP cc_start: 0.9063 (t0) cc_final: 0.8753 (t0) REVERT: C 134 ASN cc_start: 0.9685 (m-40) cc_final: 0.9398 (m110) REVERT: D 26 ARG cc_start: 0.9548 (mtm-85) cc_final: 0.9207 (ptp-110) REVERT: D 37 LYS cc_start: 0.9305 (tptt) cc_final: 0.9064 (tptp) REVERT: D 44 TYR cc_start: 0.9173 (t80) cc_final: 0.8808 (t80) REVERT: D 58 GLN cc_start: 0.9484 (mp10) cc_final: 0.9186 (mm-40) REVERT: D 66 LEU cc_start: 0.9673 (tt) cc_final: 0.9278 (mm) REVERT: D 82 GLU cc_start: 0.9535 (tt0) cc_final: 0.9130 (tm-30) REVERT: D 90 SER cc_start: 0.9450 (m) cc_final: 0.9247 (p) REVERT: D 131 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8845 (mt-10) REVERT: E 42 GLU cc_start: 0.8561 (pt0) cc_final: 0.8310 (pm20) REVERT: E 48 SER cc_start: 0.9754 (m) cc_final: 0.9509 (p) REVERT: E 55 SER cc_start: 0.9762 (m) cc_final: 0.9487 (p) REVERT: E 56 PHE cc_start: 0.9426 (t80) cc_final: 0.9165 (t80) REVERT: E 82 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9035 (tm-30) REVERT: E 101 ASN cc_start: 0.9476 (m110) cc_final: 0.9089 (m110) REVERT: E 105 TYR cc_start: 0.9286 (m-10) cc_final: 0.8815 (m-80) REVERT: E 114 THR cc_start: 0.9450 (m) cc_final: 0.9173 (p) REVERT: E 130 LYS cc_start: 0.9522 (ptmt) cc_final: 0.9240 (ttpp) REVERT: E 131 GLU cc_start: 0.9083 (tp30) cc_final: 0.8604 (tm-30) REVERT: E 134 ASN cc_start: 0.9463 (m-40) cc_final: 0.8778 (m-40) REVERT: E 135 ILE cc_start: 0.9577 (mm) cc_final: 0.9218 (mm) REVERT: J 40 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8779 (mmmm) REVERT: J 46 MET cc_start: 0.8317 (mtp) cc_final: 0.7934 (mtt) REVERT: J 82 MET cc_start: 0.8672 (mmt) cc_final: 0.8462 (mmt) REVERT: J 99 MET cc_start: 0.9454 (ttp) cc_final: 0.9125 (ppp) REVERT: J 146 PHE cc_start: 0.9236 (m-80) cc_final: 0.8941 (m-80) REVERT: J 159 MET cc_start: 0.8836 (tpp) cc_final: 0.8536 (tpp) REVERT: J 166 SER cc_start: 0.9039 (m) cc_final: 0.8586 (t) REVERT: J 209 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8496 (mp0) REVERT: J 229 MET cc_start: 0.8530 (mtp) cc_final: 0.8168 (mtp) REVERT: L 40 LYS cc_start: 0.9317 (tttt) cc_final: 0.9057 (tttp) REVERT: L 113 LYS cc_start: 0.9414 (ttmm) cc_final: 0.9116 (tppt) REVERT: N 49 MET cc_start: 0.9601 (tmm) cc_final: 0.9279 (tmm) REVERT: N 155 MET cc_start: 0.8839 (pmm) cc_final: 0.8534 (pmm) REVERT: N 161 THR cc_start: 0.9043 (p) cc_final: 0.8816 (p) REVERT: N 196 GLU cc_start: 0.8371 (tp30) cc_final: 0.7696 (tp30) REVERT: N 229 GLU cc_start: 0.8207 (tp30) cc_final: 0.7761 (tp30) REVERT: N 249 ARG cc_start: 0.9039 (ptm-80) cc_final: 0.8528 (ptm-80) REVERT: G 40 ASP cc_start: 0.9050 (m-30) cc_final: 0.8825 (p0) REVERT: G 66 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9048 (mt-10) REVERT: G 137 MET cc_start: 0.8973 (mpp) cc_final: 0.8667 (mpp) REVERT: G 169 MET cc_start: 0.8076 (mmm) cc_final: 0.7869 (mmm) REVERT: F 33 GLN cc_start: 0.9371 (mp10) cc_final: 0.9061 (mp10) REVERT: F 73 ASN cc_start: 0.9494 (t0) cc_final: 0.9216 (t0) REVERT: F 121 TYR cc_start: 0.8764 (m-80) cc_final: 0.8476 (m-80) REVERT: F 137 MET cc_start: 0.8231 (ptp) cc_final: 0.7885 (ptp) REVERT: F 200 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8828 (mp0) REVERT: F 207 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7199 (mtp85) REVERT: F 239 LYS cc_start: 0.9559 (mmtm) cc_final: 0.9327 (mmmm) REVERT: H 56 ILE cc_start: 0.9403 (pt) cc_final: 0.9094 (mm) REVERT: H 145 TYR cc_start: 0.8163 (p90) cc_final: 0.7929 (p90) REVERT: H 174 ASP cc_start: 0.8581 (t0) cc_final: 0.8139 (t70) REVERT: H 182 LYS cc_start: 0.9244 (ttmt) cc_final: 0.9036 (tttm) REVERT: H 200 MET cc_start: 0.9232 (tpp) cc_final: 0.8795 (mmm) REVERT: H 255 ASP cc_start: 0.9151 (m-30) cc_final: 0.8653 (p0) REVERT: H 261 MET cc_start: 0.9558 (mmp) cc_final: 0.9234 (mmm) REVERT: H 265 MET cc_start: 0.9497 (mtp) cc_final: 0.9157 (mtt) REVERT: I 17 MET cc_start: 0.8509 (tpp) cc_final: 0.8211 (tpp) REVERT: I 99 ASP cc_start: 0.9496 (m-30) cc_final: 0.9227 (p0) REVERT: I 110 GLN cc_start: 0.9639 (tp40) cc_final: 0.9354 (tp40) REVERT: I 118 TYR cc_start: 0.9051 (m-80) cc_final: 0.8246 (m-10) REVERT: I 129 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9035 (mmm) REVERT: I 152 MET cc_start: 0.7604 (mmm) cc_final: 0.7355 (mmm) REVERT: I 182 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.7905 (tptp) REVERT: I 275 TYR cc_start: 0.8947 (p90) cc_final: 0.8295 (p90) REVERT: I 277 LYS cc_start: 0.9452 (ttpt) cc_final: 0.9212 (pttt) REVERT: K 30 ASP cc_start: 0.8455 (m-30) cc_final: 0.8249 (m-30) REVERT: K 56 ASP cc_start: 0.9104 (m-30) cc_final: 0.8817 (m-30) REVERT: K 60 MET cc_start: 0.9198 (tmm) cc_final: 0.8791 (tmm) REVERT: K 61 ILE cc_start: 0.9156 (mt) cc_final: 0.8788 (mt) REVERT: K 81 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8698 (mt-10) REVERT: K 128 ARG cc_start: 0.9528 (ttm110) cc_final: 0.9120 (ptp-110) REVERT: K 220 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9105 (pp) REVERT: K 273 LYS cc_start: 0.9422 (tppt) cc_final: 0.8937 (mttm) REVERT: K 274 GLU cc_start: 0.8762 (mp0) cc_final: 0.8143 (mp0) REVERT: K 314 TYR cc_start: 0.8591 (m-80) cc_final: 0.8137 (m-80) REVERT: K 330 PHE cc_start: 0.9146 (m-80) cc_final: 0.8483 (m-80) REVERT: K 336 MET cc_start: 0.8862 (mmm) cc_final: 0.8428 (mmm) REVERT: K 369 ILE cc_start: 0.9380 (mt) cc_final: 0.8945 (mm) REVERT: K 386 VAL cc_start: 0.9090 (m) cc_final: 0.8824 (m) REVERT: K 406 SER cc_start: 0.9182 (m) cc_final: 0.8943 (p) REVERT: K 435 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8287 (t80) REVERT: K 438 MET cc_start: 0.8741 (mmt) cc_final: 0.8358 (mmt) REVERT: K 474 ARG cc_start: 0.2982 (mtt180) cc_final: 0.2310 (mtt180) REVERT: K 481 LEU cc_start: 0.8582 (tp) cc_final: 0.8265 (tp) REVERT: K 527 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8734 (mmtt) REVERT: K 538 ILE cc_start: 0.9276 (tp) cc_final: 0.9040 (tp) REVERT: K 625 ILE cc_start: 0.9404 (mt) cc_final: 0.9109 (mm) REVERT: K 667 GLN cc_start: 0.9107 (pm20) cc_final: 0.8702 (pm20) REVERT: K 677 MET cc_start: 0.8850 (ttp) cc_final: 0.8448 (ttp) REVERT: K 710 LYS cc_start: 0.9143 (mtmp) cc_final: 0.8902 (ptmt) REVERT: K 727 ASP cc_start: 0.9466 (m-30) cc_final: 0.8853 (t0) REVERT: K 745 MET cc_start: 0.9018 (mpp) cc_final: 0.8755 (mpp) REVERT: M 5 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9261 (tttp) REVERT: M 16 MET cc_start: 0.8685 (mmt) cc_final: 0.8290 (mmp) REVERT: M 144 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8360 (mm110) REVERT: M 169 PHE cc_start: 0.9138 (m-10) cc_final: 0.8829 (m-80) REVERT: M 231 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8973 (mttt) outliers start: 94 outliers final: 40 residues processed: 652 average time/residue: 0.3935 time to fit residues: 413.7251 Evaluate side-chains 573 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 527 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 67 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN E 51 ASN E 134 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN N 59 ASN N 173 HIS G 21 ASN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 HIS K 100 ASN K 155 GLN K 181 HIS K 734 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.050633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042353 restraints weight = 147984.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044047 restraints weight = 75777.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045221 restraints weight = 47374.109| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 29252 Z= 0.329 Angle : 0.753 12.733 39623 Z= 0.394 Chirality : 0.046 0.267 4524 Planarity : 0.005 0.051 4852 Dihedral : 13.328 179.233 4571 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 4.56 % Allowed : 19.09 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3441 helix: 1.50 (0.14), residues: 1472 sheet: -0.23 (0.23), residues: 445 loop : -1.72 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 182 HIS 0.006 0.001 HIS L 70 PHE 0.035 0.002 PHE K 245 TYR 0.023 0.002 TYR I 195 ARG 0.008 0.001 ARG E 60 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1274) hydrogen bonds : angle 5.36980 ( 3747) SS BOND : bond 0.00499 ( 15) SS BOND : angle 2.69099 ( 30) covalent geometry : bond 0.00696 (29237) covalent geometry : angle 0.75006 (39593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 514 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8772 (m-30) cc_final: 0.8286 (t0) REVERT: A 42 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 56 PHE cc_start: 0.9000 (t80) cc_final: 0.8606 (t80) REVERT: A 60 ARG cc_start: 0.9295 (mmp80) cc_final: 0.8895 (mmm160) REVERT: A 69 TYR cc_start: 0.9293 (t80) cc_final: 0.9064 (t80) REVERT: A 79 ILE cc_start: 0.9024 (mm) cc_final: 0.8760 (mp) REVERT: A 110 TYR cc_start: 0.9065 (t80) cc_final: 0.8837 (t80) REVERT: A 111 ASP cc_start: 0.9033 (t0) cc_final: 0.8699 (t0) REVERT: A 131 GLU cc_start: 0.9447 (mt-10) cc_final: 0.8939 (mt-10) REVERT: B 22 ASP cc_start: 0.8908 (m-30) cc_final: 0.8179 (m-30) REVERT: B 26 ARG cc_start: 0.9133 (ptp-110) cc_final: 0.8400 (ptp90) REVERT: B 73 GLN cc_start: 0.9288 (tp40) cc_final: 0.9005 (tp-100) REVERT: B 78 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8698 (tp30) REVERT: B 90 SER cc_start: 0.9643 (m) cc_final: 0.9241 (p) REVERT: B 129 PHE cc_start: 0.9273 (t80) cc_final: 0.8899 (t80) REVERT: B 134 ASN cc_start: 0.9234 (m-40) cc_final: 0.8914 (m110) REVERT: C 22 ASP cc_start: 0.9201 (m-30) cc_final: 0.8910 (m-30) REVERT: C 44 TYR cc_start: 0.9261 (t80) cc_final: 0.8952 (t80) REVERT: C 45 VAL cc_start: 0.9581 (t) cc_final: 0.9357 (p) REVERT: C 71 MET cc_start: 0.9436 (mtm) cc_final: 0.9100 (mtm) REVERT: C 77 ASP cc_start: 0.9143 (t0) cc_final: 0.8828 (t0) REVERT: C 103 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9463 (tp) REVERT: C 105 TYR cc_start: 0.9368 (m-80) cc_final: 0.9136 (m-80) REVERT: C 134 ASN cc_start: 0.9740 (m-40) cc_final: 0.9439 (m110) REVERT: D 26 ARG cc_start: 0.9582 (mtm-85) cc_final: 0.9262 (ptp90) REVERT: D 37 LYS cc_start: 0.9325 (tptt) cc_final: 0.9097 (tptp) REVERT: D 44 TYR cc_start: 0.9250 (t80) cc_final: 0.8719 (t80) REVERT: D 58 GLN cc_start: 0.9503 (mp10) cc_final: 0.9284 (mm-40) REVERT: D 82 GLU cc_start: 0.9533 (tt0) cc_final: 0.9298 (tm-30) REVERT: D 90 SER cc_start: 0.9540 (m) cc_final: 0.9328 (p) REVERT: D 131 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8743 (mt-10) REVERT: E 42 GLU cc_start: 0.8695 (pt0) cc_final: 0.8401 (pm20) REVERT: E 48 SER cc_start: 0.9772 (m) cc_final: 0.9570 (p) REVERT: E 78 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8029 (mt-10) REVERT: E 82 GLU cc_start: 0.9373 (tm-30) cc_final: 0.9025 (tm-30) REVERT: E 94 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8571 (mtt90) REVERT: E 101 ASN cc_start: 0.9574 (m110) cc_final: 0.9174 (m110) REVERT: E 105 TYR cc_start: 0.9342 (m-10) cc_final: 0.8889 (m-80) REVERT: E 114 THR cc_start: 0.9535 (m) cc_final: 0.9281 (p) REVERT: E 131 GLU cc_start: 0.9104 (tp30) cc_final: 0.8747 (tm-30) REVERT: E 135 ILE cc_start: 0.9615 (mm) cc_final: 0.9286 (mm) REVERT: J 57 GLU cc_start: 0.8293 (mp0) cc_final: 0.7805 (tm-30) REVERT: J 146 PHE cc_start: 0.9233 (m-80) cc_final: 0.8879 (m-80) REVERT: J 159 MET cc_start: 0.8964 (tpp) cc_final: 0.8640 (tpp) REVERT: J 166 SER cc_start: 0.9139 (m) cc_final: 0.8717 (t) REVERT: J 209 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8491 (mp0) REVERT: J 229 MET cc_start: 0.8693 (mtp) cc_final: 0.8340 (mtp) REVERT: L 83 TYR cc_start: 0.7863 (m-80) cc_final: 0.7644 (m-10) REVERT: L 113 LYS cc_start: 0.9496 (ttmm) cc_final: 0.9217 (tppt) REVERT: L 118 LYS cc_start: 0.9620 (tppp) cc_final: 0.9299 (tppt) REVERT: N 49 MET cc_start: 0.9625 (tmm) cc_final: 0.9300 (tmm) REVERT: N 137 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7648 (p90) REVERT: N 146 ASP cc_start: 0.8726 (m-30) cc_final: 0.8314 (t0) REVERT: N 155 MET cc_start: 0.8881 (pmm) cc_final: 0.8621 (pmm) REVERT: N 249 ARG cc_start: 0.9167 (ptm-80) cc_final: 0.8881 (ptm-80) REVERT: G 40 ASP cc_start: 0.9143 (m-30) cc_final: 0.8854 (p0) REVERT: G 66 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8985 (mt-10) REVERT: G 137 MET cc_start: 0.8966 (mpp) cc_final: 0.8715 (mpp) REVERT: G 169 MET cc_start: 0.7902 (mmm) cc_final: 0.7599 (mmm) REVERT: F 33 GLN cc_start: 0.9339 (mp10) cc_final: 0.8972 (mp10) REVERT: F 73 ASN cc_start: 0.9563 (t0) cc_final: 0.9320 (t0) REVERT: F 137 MET cc_start: 0.8649 (ptp) cc_final: 0.8259 (mpp) REVERT: F 207 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7426 (mtp85) REVERT: F 239 LYS cc_start: 0.9557 (mmtm) cc_final: 0.9292 (mmmm) REVERT: H 19 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8164 (tm-30) REVERT: H 145 TYR cc_start: 0.8613 (p90) cc_final: 0.8093 (p90) REVERT: H 174 ASP cc_start: 0.8765 (t0) cc_final: 0.8371 (t70) REVERT: H 255 ASP cc_start: 0.9225 (m-30) cc_final: 0.8764 (p0) REVERT: I 99 ASP cc_start: 0.9563 (m-30) cc_final: 0.9248 (p0) REVERT: I 110 GLN cc_start: 0.9647 (tp40) cc_final: 0.9295 (tp-100) REVERT: I 117 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7547 (p0) REVERT: I 182 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8128 (tptp) REVERT: I 253 ASN cc_start: 0.8929 (t0) cc_final: 0.8723 (t0) REVERT: I 275 TYR cc_start: 0.9086 (p90) cc_final: 0.8531 (p90) REVERT: K 60 MET cc_start: 0.9252 (tmm) cc_final: 0.8848 (tmm) REVERT: K 61 ILE cc_start: 0.9261 (mt) cc_final: 0.8847 (mt) REVERT: K 81 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8585 (mt-10) REVERT: K 148 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8794 (t) REVERT: K 336 MET cc_start: 0.8897 (mmm) cc_final: 0.8636 (mmm) REVERT: K 369 ILE cc_start: 0.9515 (mt) cc_final: 0.9091 (mm) REVERT: K 406 SER cc_start: 0.9260 (m) cc_final: 0.9011 (p) REVERT: K 438 MET cc_start: 0.8798 (mmt) cc_final: 0.8473 (mmt) REVERT: K 447 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7889 (mt) REVERT: K 461 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.4755 (tpt90) REVERT: K 474 ARG cc_start: 0.3039 (mtt180) cc_final: 0.2599 (mtt180) REVERT: K 481 LEU cc_start: 0.8641 (tp) cc_final: 0.8287 (tp) REVERT: K 502 LYS cc_start: 0.9435 (mtpt) cc_final: 0.9120 (mtmm) REVERT: K 527 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8730 (mmmt) REVERT: K 538 ILE cc_start: 0.9405 (tp) cc_final: 0.9150 (tp) REVERT: K 587 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8741 (tppt) REVERT: K 588 MET cc_start: 0.9310 (mtm) cc_final: 0.8818 (mtp) REVERT: K 625 ILE cc_start: 0.9410 (mt) cc_final: 0.9103 (mm) REVERT: K 677 MET cc_start: 0.8944 (ttp) cc_final: 0.8692 (ttp) REVERT: K 727 ASP cc_start: 0.9527 (m-30) cc_final: 0.8887 (t0) REVERT: K 730 GLU cc_start: 0.9090 (tt0) cc_final: 0.8818 (tp30) REVERT: K 745 MET cc_start: 0.8987 (mpp) cc_final: 0.8654 (mtm) REVERT: M 5 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9261 (tttp) REVERT: M 16 MET cc_start: 0.8716 (mmt) cc_final: 0.8353 (mmp) REVERT: M 62 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9360 (mm) REVERT: M 144 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8407 (mm110) REVERT: M 169 PHE cc_start: 0.9103 (m-10) cc_final: 0.8840 (m-80) REVERT: M 170 ASP cc_start: 0.9058 (t0) cc_final: 0.8758 (t0) outliers start: 141 outliers final: 74 residues processed: 613 average time/residue: 0.3908 time to fit residues: 383.8320 Evaluate side-chains 553 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 469 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 126 GLN Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 461 ARG Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 627 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 5 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN K 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.051268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043016 restraints weight = 144884.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044706 restraints weight = 74361.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045891 restraints weight = 46513.665| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29252 Z= 0.209 Angle : 0.677 13.668 39623 Z= 0.353 Chirality : 0.044 0.261 4524 Planarity : 0.004 0.058 4852 Dihedral : 13.334 179.035 4571 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 4.08 % Allowed : 20.45 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3441 helix: 1.52 (0.14), residues: 1473 sheet: -0.26 (0.23), residues: 464 loop : -1.73 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 182 HIS 0.004 0.001 HIS M 146 PHE 0.038 0.002 PHE E 56 TYR 0.032 0.002 TYR K 62 ARG 0.016 0.000 ARG I 165 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1274) hydrogen bonds : angle 5.19457 ( 3747) SS BOND : bond 0.00452 ( 15) SS BOND : angle 2.05541 ( 30) covalent geometry : bond 0.00451 (29237) covalent geometry : angle 0.67530 (39593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 507 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8747 (m-30) cc_final: 0.8262 (t0) REVERT: A 42 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 56 PHE cc_start: 0.8966 (t80) cc_final: 0.8579 (t80) REVERT: A 60 ARG cc_start: 0.9293 (mmp80) cc_final: 0.8901 (mmm160) REVERT: A 69 TYR cc_start: 0.9271 (t80) cc_final: 0.9051 (t80) REVERT: A 79 ILE cc_start: 0.9033 (mm) cc_final: 0.8751 (mp) REVERT: A 110 TYR cc_start: 0.9049 (t80) cc_final: 0.8792 (t80) REVERT: A 111 ASP cc_start: 0.8995 (t0) cc_final: 0.8655 (t0) REVERT: A 131 GLU cc_start: 0.9443 (mt-10) cc_final: 0.8914 (mt-10) REVERT: B 22 ASP cc_start: 0.8932 (m-30) cc_final: 0.8272 (m-30) REVERT: B 26 ARG cc_start: 0.9128 (ptp-110) cc_final: 0.8401 (ptp90) REVERT: B 73 GLN cc_start: 0.9276 (tp40) cc_final: 0.8992 (tp-100) REVERT: B 78 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8608 (tp30) REVERT: B 90 SER cc_start: 0.9631 (m) cc_final: 0.9226 (p) REVERT: B 129 PHE cc_start: 0.9118 (t80) cc_final: 0.8858 (t80) REVERT: B 134 ASN cc_start: 0.9217 (m-40) cc_final: 0.8865 (m110) REVERT: C 22 ASP cc_start: 0.9182 (m-30) cc_final: 0.8919 (m-30) REVERT: C 44 TYR cc_start: 0.9221 (t80) cc_final: 0.8806 (t80) REVERT: C 45 VAL cc_start: 0.9596 (t) cc_final: 0.9339 (p) REVERT: C 71 MET cc_start: 0.9410 (mtm) cc_final: 0.9054 (mtm) REVERT: C 77 ASP cc_start: 0.9192 (t0) cc_final: 0.8908 (t0) REVERT: C 134 ASN cc_start: 0.9729 (m-40) cc_final: 0.9416 (m110) REVERT: D 32 ILE cc_start: 0.9139 (tp) cc_final: 0.8928 (tp) REVERT: D 37 LYS cc_start: 0.9362 (tptt) cc_final: 0.9101 (tptp) REVERT: D 44 TYR cc_start: 0.9194 (t80) cc_final: 0.8763 (t80) REVERT: D 58 GLN cc_start: 0.9506 (mp10) cc_final: 0.9275 (mm-40) REVERT: D 82 GLU cc_start: 0.9495 (tt0) cc_final: 0.9111 (tp30) REVERT: D 90 SER cc_start: 0.9508 (m) cc_final: 0.9291 (p) REVERT: D 131 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8750 (mt-10) REVERT: E 48 SER cc_start: 0.9758 (m) cc_final: 0.9548 (p) REVERT: E 55 SER cc_start: 0.9786 (m) cc_final: 0.9527 (p) REVERT: E 78 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8164 (mt-10) REVERT: E 82 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8986 (tm-30) REVERT: E 101 ASN cc_start: 0.9557 (m110) cc_final: 0.9169 (m110) REVERT: E 105 TYR cc_start: 0.9304 (m-10) cc_final: 0.8868 (m-80) REVERT: E 114 THR cc_start: 0.9531 (m) cc_final: 0.9268 (p) REVERT: E 131 GLU cc_start: 0.9025 (tp30) cc_final: 0.8642 (tm-30) REVERT: E 135 ILE cc_start: 0.9599 (mm) cc_final: 0.9237 (mm) REVERT: J 146 PHE cc_start: 0.9237 (m-80) cc_final: 0.8901 (m-80) REVERT: J 159 MET cc_start: 0.8889 (tpp) cc_final: 0.8595 (tpp) REVERT: J 166 SER cc_start: 0.9115 (m) cc_final: 0.8685 (t) REVERT: J 229 MET cc_start: 0.8662 (mtp) cc_final: 0.8262 (mtp) REVERT: L 113 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9206 (tppt) REVERT: L 118 LYS cc_start: 0.9635 (tppp) cc_final: 0.9289 (tppp) REVERT: N 49 MET cc_start: 0.9605 (tmm) cc_final: 0.9306 (tmm) REVERT: N 137 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7416 (p90) REVERT: N 249 ARG cc_start: 0.9253 (ptm-80) cc_final: 0.8912 (ptm-80) REVERT: G 40 ASP cc_start: 0.9102 (m-30) cc_final: 0.8829 (p0) REVERT: G 66 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8967 (mt-10) REVERT: G 137 MET cc_start: 0.8971 (mpp) cc_final: 0.8657 (mpp) REVERT: F 33 GLN cc_start: 0.9366 (mp10) cc_final: 0.8957 (mp10) REVERT: F 73 ASN cc_start: 0.9529 (t0) cc_final: 0.9282 (t0) REVERT: F 137 MET cc_start: 0.8578 (ptp) cc_final: 0.8198 (ptp) REVERT: F 207 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7371 (mtp85) REVERT: F 239 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9261 (mmmm) REVERT: H 5 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8778 (m) REVERT: H 19 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8134 (tm-30) REVERT: H 145 TYR cc_start: 0.8548 (p90) cc_final: 0.8104 (p90) REVERT: H 174 ASP cc_start: 0.8772 (t0) cc_final: 0.8363 (t70) REVERT: H 255 ASP cc_start: 0.9204 (m-30) cc_final: 0.8801 (p0) REVERT: H 265 MET cc_start: 0.9495 (mtp) cc_final: 0.9219 (mtt) REVERT: I 99 ASP cc_start: 0.9541 (m-30) cc_final: 0.9192 (p0) REVERT: I 110 GLN cc_start: 0.9648 (tp40) cc_final: 0.9358 (tp40) REVERT: I 253 ASN cc_start: 0.8944 (t0) cc_final: 0.8678 (t0) REVERT: I 265 MET cc_start: 0.9665 (mtm) cc_final: 0.9346 (mtm) REVERT: I 275 TYR cc_start: 0.9005 (p90) cc_final: 0.8365 (p90) REVERT: K 60 MET cc_start: 0.9313 (tmm) cc_final: 0.8877 (tmm) REVERT: K 61 ILE cc_start: 0.9222 (mt) cc_final: 0.8799 (mt) REVERT: K 81 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8595 (mt-10) REVERT: K 220 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9251 (pp) REVERT: K 273 LYS cc_start: 0.9457 (tppt) cc_final: 0.8902 (mttm) REVERT: K 336 MET cc_start: 0.8893 (mmm) cc_final: 0.8615 (mmm) REVERT: K 369 ILE cc_start: 0.9300 (mt) cc_final: 0.8848 (mt) REVERT: K 406 SER cc_start: 0.9233 (m) cc_final: 0.8997 (p) REVERT: K 435 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8322 (t80) REVERT: K 438 MET cc_start: 0.8857 (mmt) cc_final: 0.8451 (mmt) REVERT: K 447 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7993 (mt) REVERT: K 474 ARG cc_start: 0.3030 (mtt180) cc_final: 0.2393 (mtt180) REVERT: K 481 LEU cc_start: 0.8659 (tp) cc_final: 0.8302 (tp) REVERT: K 502 LYS cc_start: 0.9397 (mtpt) cc_final: 0.9085 (mtmm) REVERT: K 527 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8511 (mmmt) REVERT: K 538 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9093 (tp) REVERT: K 587 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8743 (tppt) REVERT: K 588 MET cc_start: 0.9330 (mtm) cc_final: 0.8840 (mtp) REVERT: K 625 ILE cc_start: 0.9398 (mt) cc_final: 0.9072 (mm) REVERT: K 667 GLN cc_start: 0.9195 (pm20) cc_final: 0.8827 (pm20) REVERT: K 677 MET cc_start: 0.8932 (ttp) cc_final: 0.8438 (ttp) REVERT: K 727 ASP cc_start: 0.9489 (m-30) cc_final: 0.8849 (t0) REVERT: K 730 GLU cc_start: 0.9060 (tt0) cc_final: 0.8758 (tp30) REVERT: K 745 MET cc_start: 0.8986 (mpp) cc_final: 0.8670 (mtm) REVERT: K 765 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9208 (tt) REVERT: M 5 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9262 (ptmm) REVERT: M 16 MET cc_start: 0.8743 (mmt) cc_final: 0.8384 (mmp) REVERT: M 62 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9369 (mm) REVERT: M 103 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: M 144 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8357 (mm110) REVERT: M 169 PHE cc_start: 0.9083 (m-10) cc_final: 0.8790 (m-80) REVERT: M 170 ASP cc_start: 0.9040 (t0) cc_final: 0.8722 (t0) REVERT: M 290 MET cc_start: 0.8954 (pmm) cc_final: 0.8697 (pmm) outliers start: 126 outliers final: 82 residues processed: 594 average time/residue: 0.3932 time to fit residues: 379.3411 Evaluate side-chains 566 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 473 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 212 MET Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 627 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 765 LEU Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 267 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 309 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044696 restraints weight = 141925.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046443 restraints weight = 72491.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047654 restraints weight = 45101.497| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29252 Z= 0.133 Angle : 0.657 16.718 39623 Z= 0.337 Chirality : 0.044 0.270 4524 Planarity : 0.004 0.056 4852 Dihedral : 13.298 179.598 4571 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 3.07 % Allowed : 21.39 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3441 helix: 1.57 (0.14), residues: 1467 sheet: -0.12 (0.23), residues: 454 loop : -1.66 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 182 HIS 0.006 0.001 HIS K 153 PHE 0.025 0.001 PHE E 56 TYR 0.045 0.002 TYR K 62 ARG 0.006 0.000 ARG K 244 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1274) hydrogen bonds : angle 4.97680 ( 3747) SS BOND : bond 0.00437 ( 15) SS BOND : angle 1.91199 ( 30) covalent geometry : bond 0.00300 (29237) covalent geometry : angle 0.65546 (39593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 521 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8725 (m-30) cc_final: 0.8241 (t0) REVERT: A 42 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 56 PHE cc_start: 0.8939 (t80) cc_final: 0.8585 (t80) REVERT: A 60 ARG cc_start: 0.9293 (mmp80) cc_final: 0.8899 (mmm160) REVERT: A 79 ILE cc_start: 0.9006 (mm) cc_final: 0.8714 (mp) REVERT: A 110 TYR cc_start: 0.9024 (t80) cc_final: 0.8818 (t80) REVERT: A 111 ASP cc_start: 0.9019 (t0) cc_final: 0.8664 (t0) REVERT: A 131 GLU cc_start: 0.9441 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 22 ASP cc_start: 0.8847 (m-30) cc_final: 0.8125 (m-30) REVERT: B 26 ARG cc_start: 0.9139 (ptp-110) cc_final: 0.8417 (ptp90) REVERT: B 44 TYR cc_start: 0.9301 (t80) cc_final: 0.8954 (t80) REVERT: B 73 GLN cc_start: 0.9274 (tp40) cc_final: 0.9054 (tp-100) REVERT: B 78 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8488 (tp30) REVERT: B 90 SER cc_start: 0.9661 (m) cc_final: 0.9276 (p) REVERT: B 129 PHE cc_start: 0.8906 (t80) cc_final: 0.8643 (t80) REVERT: B 131 GLU cc_start: 0.9214 (mp0) cc_final: 0.8807 (pm20) REVERT: B 134 ASN cc_start: 0.9139 (m-40) cc_final: 0.8706 (m110) REVERT: C 22 ASP cc_start: 0.9211 (m-30) cc_final: 0.8943 (m-30) REVERT: C 44 TYR cc_start: 0.9160 (t80) cc_final: 0.8552 (t80) REVERT: C 45 VAL cc_start: 0.9525 (t) cc_final: 0.9207 (p) REVERT: C 71 MET cc_start: 0.9378 (mtm) cc_final: 0.9036 (mtm) REVERT: C 77 ASP cc_start: 0.9259 (t0) cc_final: 0.9009 (t0) REVERT: C 103 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9303 (tp) REVERT: C 105 TYR cc_start: 0.9361 (m-80) cc_final: 0.9121 (m-80) REVERT: C 134 ASN cc_start: 0.9717 (m-40) cc_final: 0.9406 (m110) REVERT: D 26 ARG cc_start: 0.9502 (mtm-85) cc_final: 0.9296 (ptp-110) REVERT: D 32 ILE cc_start: 0.9133 (tp) cc_final: 0.8873 (tp) REVERT: D 37 LYS cc_start: 0.9351 (tptt) cc_final: 0.9073 (tptp) REVERT: D 44 TYR cc_start: 0.9140 (t80) cc_final: 0.8687 (t80) REVERT: D 58 GLN cc_start: 0.9500 (mp10) cc_final: 0.9157 (mm-40) REVERT: D 66 LEU cc_start: 0.9691 (tt) cc_final: 0.9342 (mm) REVERT: D 82 GLU cc_start: 0.9490 (tt0) cc_final: 0.9036 (tp30) REVERT: D 90 SER cc_start: 0.9433 (m) cc_final: 0.9223 (p) REVERT: D 95 GLU cc_start: 0.8512 (tp30) cc_final: 0.8169 (tm-30) REVERT: D 98 ASP cc_start: 0.9537 (m-30) cc_final: 0.9242 (m-30) REVERT: D 101 ASN cc_start: 0.9566 (m110) cc_final: 0.9330 (m110) REVERT: D 131 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8802 (mt-10) REVERT: E 44 TYR cc_start: 0.8983 (t80) cc_final: 0.8747 (t80) REVERT: E 48 SER cc_start: 0.9747 (m) cc_final: 0.9529 (p) REVERT: E 55 SER cc_start: 0.9768 (m) cc_final: 0.9492 (p) REVERT: E 56 PHE cc_start: 0.9477 (t80) cc_final: 0.9200 (t80) REVERT: E 78 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8291 (mt-10) REVERT: E 82 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8955 (tm-30) REVERT: E 101 ASN cc_start: 0.9534 (m110) cc_final: 0.9125 (m110) REVERT: E 105 TYR cc_start: 0.9266 (m-10) cc_final: 0.8800 (m-80) REVERT: E 114 THR cc_start: 0.9483 (m) cc_final: 0.9222 (p) REVERT: E 131 GLU cc_start: 0.9016 (tp30) cc_final: 0.8607 (tm-30) REVERT: E 135 ILE cc_start: 0.9583 (mm) cc_final: 0.9228 (mm) REVERT: J 57 GLU cc_start: 0.8259 (mp0) cc_final: 0.7914 (tm-30) REVERT: J 99 MET cc_start: 0.9439 (ttp) cc_final: 0.9223 (ppp) REVERT: J 146 PHE cc_start: 0.9250 (m-80) cc_final: 0.8919 (m-80) REVERT: J 159 MET cc_start: 0.8883 (tpp) cc_final: 0.8579 (tpp) REVERT: J 166 SER cc_start: 0.9074 (m) cc_final: 0.8781 (t) REVERT: J 209 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8552 (mp0) REVERT: L 43 MET cc_start: 0.8871 (ttp) cc_final: 0.8619 (tpp) REVERT: L 113 LYS cc_start: 0.9459 (ttmm) cc_final: 0.9214 (tppp) REVERT: N 49 MET cc_start: 0.9581 (tmm) cc_final: 0.9299 (tmm) REVERT: N 137 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7208 (p90) REVERT: N 249 ARG cc_start: 0.9238 (ptm-80) cc_final: 0.8910 (ptm-80) REVERT: G 40 ASP cc_start: 0.9089 (m-30) cc_final: 0.8830 (p0) REVERT: G 66 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8955 (mt-10) REVERT: G 137 MET cc_start: 0.8978 (mpp) cc_final: 0.8601 (mpp) REVERT: F 33 GLN cc_start: 0.9413 (mp10) cc_final: 0.8977 (mp10) REVERT: F 73 ASN cc_start: 0.9518 (t0) cc_final: 0.9253 (t0) REVERT: F 121 TYR cc_start: 0.8754 (m-80) cc_final: 0.8260 (m-80) REVERT: F 137 MET cc_start: 0.8468 (ptp) cc_final: 0.8162 (mpp) REVERT: F 239 LYS cc_start: 0.9560 (mmtm) cc_final: 0.9300 (mmmm) REVERT: H 5 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8683 (m) REVERT: H 19 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8126 (tm-30) REVERT: H 129 MET cc_start: 0.9275 (tpt) cc_final: 0.9064 (tpp) REVERT: H 145 TYR cc_start: 0.8414 (p90) cc_final: 0.7967 (p90) REVERT: H 174 ASP cc_start: 0.8739 (t0) cc_final: 0.8302 (t70) REVERT: H 255 ASP cc_start: 0.9205 (m-30) cc_final: 0.8694 (p0) REVERT: H 265 MET cc_start: 0.9402 (mtp) cc_final: 0.9057 (mtm) REVERT: I 99 ASP cc_start: 0.9510 (m-30) cc_final: 0.9145 (p0) REVERT: I 110 GLN cc_start: 0.9640 (tp40) cc_final: 0.9300 (tp40) REVERT: I 200 MET cc_start: 0.8984 (ttp) cc_final: 0.8679 (ttp) REVERT: I 275 TYR cc_start: 0.8929 (p90) cc_final: 0.8243 (p90) REVERT: K 60 MET cc_start: 0.9176 (tmm) cc_final: 0.8766 (tmm) REVERT: K 61 ILE cc_start: 0.9158 (mt) cc_final: 0.8742 (mt) REVERT: K 220 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9170 (pp) REVERT: K 273 LYS cc_start: 0.9408 (tppt) cc_final: 0.8922 (mttm) REVERT: K 336 MET cc_start: 0.8872 (mmm) cc_final: 0.8515 (mmm) REVERT: K 369 ILE cc_start: 0.9317 (mt) cc_final: 0.8879 (mt) REVERT: K 406 SER cc_start: 0.9215 (m) cc_final: 0.8986 (p) REVERT: K 438 MET cc_start: 0.8911 (mmt) cc_final: 0.8459 (mmt) REVERT: K 447 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8237 (mt) REVERT: K 474 ARG cc_start: 0.2884 (mtt180) cc_final: 0.2384 (mtt180) REVERT: K 481 LEU cc_start: 0.8646 (tp) cc_final: 0.8298 (tp) REVERT: K 527 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8600 (mmmt) REVERT: K 538 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9013 (tp) REVERT: K 587 LYS cc_start: 0.9256 (mmtm) cc_final: 0.8746 (tppt) REVERT: K 588 MET cc_start: 0.9333 (mtm) cc_final: 0.8829 (mtp) REVERT: K 625 ILE cc_start: 0.9414 (mt) cc_final: 0.9083 (mm) REVERT: K 667 GLN cc_start: 0.9142 (pm20) cc_final: 0.8797 (pm20) REVERT: K 677 MET cc_start: 0.8891 (ttp) cc_final: 0.8606 (ttp) REVERT: K 727 ASP cc_start: 0.9495 (m-30) cc_final: 0.8850 (t0) REVERT: K 730 GLU cc_start: 0.9061 (tt0) cc_final: 0.8717 (tp30) REVERT: K 745 MET cc_start: 0.9070 (mpp) cc_final: 0.8729 (mtm) REVERT: M 5 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9284 (tttp) REVERT: M 16 MET cc_start: 0.8722 (mmt) cc_final: 0.8336 (mmp) REVERT: M 62 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9363 (mm) REVERT: M 169 PHE cc_start: 0.9035 (m-10) cc_final: 0.8726 (m-80) outliers start: 95 outliers final: 61 residues processed: 587 average time/residue: 0.3948 time to fit residues: 378.4962 Evaluate side-chains 553 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 342 optimal weight: 5.9990 chunk 272 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 134 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044884 restraints weight = 142280.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.046629 restraints weight = 72458.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047824 restraints weight = 44929.377| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29252 Z= 0.139 Angle : 0.659 14.864 39623 Z= 0.335 Chirality : 0.044 0.328 4524 Planarity : 0.004 0.058 4852 Dihedral : 13.275 177.805 4571 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 3.20 % Allowed : 22.27 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3441 helix: 1.53 (0.14), residues: 1470 sheet: -0.11 (0.23), residues: 458 loop : -1.64 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 182 HIS 0.003 0.001 HIS L 70 PHE 0.033 0.001 PHE E 129 TYR 0.031 0.002 TYR K 62 ARG 0.007 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 1274) hydrogen bonds : angle 4.94988 ( 3747) SS BOND : bond 0.00336 ( 15) SS BOND : angle 1.80496 ( 30) covalent geometry : bond 0.00306 (29237) covalent geometry : angle 0.65730 (39593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 512 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8708 (m-30) cc_final: 0.8215 (t0) REVERT: A 42 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8108 (mm-30) REVERT: A 56 PHE cc_start: 0.8926 (t80) cc_final: 0.8536 (t80) REVERT: A 60 ARG cc_start: 0.9276 (mmp80) cc_final: 0.8916 (mmm-85) REVERT: A 69 TYR cc_start: 0.9153 (t80) cc_final: 0.8870 (t80) REVERT: A 79 ILE cc_start: 0.9012 (mm) cc_final: 0.8710 (mp) REVERT: A 110 TYR cc_start: 0.9025 (t80) cc_final: 0.8821 (t80) REVERT: A 111 ASP cc_start: 0.9022 (t0) cc_final: 0.8672 (t0) REVERT: A 131 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8919 (mt-10) REVERT: B 22 ASP cc_start: 0.8846 (m-30) cc_final: 0.8199 (m-30) REVERT: B 26 ARG cc_start: 0.9135 (ptp-110) cc_final: 0.8475 (ptp90) REVERT: B 44 TYR cc_start: 0.9287 (t80) cc_final: 0.8896 (t80) REVERT: B 69 TYR cc_start: 0.8994 (t80) cc_final: 0.8597 (t80) REVERT: B 73 GLN cc_start: 0.9338 (tp40) cc_final: 0.9075 (tp-100) REVERT: B 78 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8210 (tp30) REVERT: B 90 SER cc_start: 0.9660 (m) cc_final: 0.9280 (p) REVERT: B 131 GLU cc_start: 0.9223 (mp0) cc_final: 0.8845 (pm20) REVERT: B 134 ASN cc_start: 0.9139 (m-40) cc_final: 0.8716 (m110) REVERT: C 22 ASP cc_start: 0.9243 (m-30) cc_final: 0.8989 (m-30) REVERT: C 44 TYR cc_start: 0.9113 (t80) cc_final: 0.8702 (t80) REVERT: C 45 VAL cc_start: 0.9511 (t) cc_final: 0.9167 (p) REVERT: C 71 MET cc_start: 0.9358 (mtm) cc_final: 0.9046 (mtm) REVERT: C 77 ASP cc_start: 0.9261 (t0) cc_final: 0.9029 (t0) REVERT: C 103 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9370 (tp) REVERT: C 105 TYR cc_start: 0.9367 (m-80) cc_final: 0.9112 (m-80) REVERT: C 134 ASN cc_start: 0.9723 (m-40) cc_final: 0.9407 (m110) REVERT: D 26 ARG cc_start: 0.9543 (mtm-85) cc_final: 0.9290 (ptp-110) REVERT: D 32 ILE cc_start: 0.9153 (tp) cc_final: 0.8926 (tp) REVERT: D 37 LYS cc_start: 0.9346 (tptt) cc_final: 0.9091 (tptp) REVERT: D 44 TYR cc_start: 0.9085 (t80) cc_final: 0.8669 (t80) REVERT: D 58 GLN cc_start: 0.9468 (mp10) cc_final: 0.9132 (mm-40) REVERT: D 82 GLU cc_start: 0.9497 (tt0) cc_final: 0.9036 (tp30) REVERT: D 90 SER cc_start: 0.9435 (m) cc_final: 0.9227 (p) REVERT: D 101 ASN cc_start: 0.9548 (m110) cc_final: 0.9313 (m110) REVERT: D 131 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8877 (mt-10) REVERT: E 44 TYR cc_start: 0.9053 (t80) cc_final: 0.8835 (t80) REVERT: E 55 SER cc_start: 0.9767 (m) cc_final: 0.9482 (p) REVERT: E 56 PHE cc_start: 0.9495 (t80) cc_final: 0.9209 (t80) REVERT: E 78 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8291 (mt-10) REVERT: E 82 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8997 (tm-30) REVERT: E 101 ASN cc_start: 0.9521 (m110) cc_final: 0.9127 (m110) REVERT: E 105 TYR cc_start: 0.9266 (m-10) cc_final: 0.8831 (m-80) REVERT: E 114 THR cc_start: 0.9414 (m) cc_final: 0.9110 (p) REVERT: E 131 GLU cc_start: 0.9031 (tp30) cc_final: 0.8614 (tm-30) REVERT: E 135 ILE cc_start: 0.9596 (mm) cc_final: 0.9242 (mm) REVERT: J 99 MET cc_start: 0.9454 (ttp) cc_final: 0.9161 (ppp) REVERT: J 146 PHE cc_start: 0.9224 (m-80) cc_final: 0.8892 (m-80) REVERT: J 159 MET cc_start: 0.8973 (tpp) cc_final: 0.8674 (tpp) REVERT: J 209 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8490 (mp0) REVERT: L 43 MET cc_start: 0.8865 (ttp) cc_final: 0.8588 (tpp) REVERT: L 104 TYR cc_start: 0.8610 (p90) cc_final: 0.8296 (p90) REVERT: L 113 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9233 (tppp) REVERT: L 115 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8723 (mm110) REVERT: L 118 LYS cc_start: 0.9585 (ttmm) cc_final: 0.9140 (ttmm) REVERT: N 49 MET cc_start: 0.9588 (tmm) cc_final: 0.9298 (tmm) REVERT: N 137 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7221 (p90) REVERT: N 155 MET cc_start: 0.9028 (pmm) cc_final: 0.8802 (pmm) REVERT: N 249 ARG cc_start: 0.9237 (ptm-80) cc_final: 0.8916 (ptm-80) REVERT: G 40 ASP cc_start: 0.9099 (m-30) cc_final: 0.8823 (p0) REVERT: G 66 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8967 (mt-10) REVERT: G 137 MET cc_start: 0.8965 (mpp) cc_final: 0.8606 (mpp) REVERT: F 33 GLN cc_start: 0.9420 (mp10) cc_final: 0.8989 (mp10) REVERT: F 73 ASN cc_start: 0.9529 (t0) cc_final: 0.9267 (t0) REVERT: F 137 MET cc_start: 0.8479 (ptp) cc_final: 0.8152 (mpp) REVERT: F 239 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9291 (mmmm) REVERT: H 5 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8700 (m) REVERT: H 19 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8086 (tm-30) REVERT: H 129 MET cc_start: 0.9288 (tpt) cc_final: 0.9077 (tpp) REVERT: H 145 TYR cc_start: 0.8413 (p90) cc_final: 0.7956 (p90) REVERT: H 174 ASP cc_start: 0.8709 (t0) cc_final: 0.8265 (t70) REVERT: H 255 ASP cc_start: 0.9218 (m-30) cc_final: 0.8692 (p0) REVERT: H 265 MET cc_start: 0.9269 (mtp) cc_final: 0.8990 (mtm) REVERT: H 266 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9103 (mp0) REVERT: I 17 MET cc_start: 0.8766 (mmm) cc_final: 0.8536 (tpp) REVERT: I 99 ASP cc_start: 0.9519 (m-30) cc_final: 0.9166 (p0) REVERT: I 110 GLN cc_start: 0.9649 (tp40) cc_final: 0.9349 (tp40) REVERT: I 129 MET cc_start: 0.8992 (mmm) cc_final: 0.8718 (mmp) REVERT: I 200 MET cc_start: 0.9026 (ttp) cc_final: 0.8686 (ttp) REVERT: I 265 MET cc_start: 0.9635 (mtm) cc_final: 0.9387 (mtm) REVERT: I 275 TYR cc_start: 0.8975 (p90) cc_final: 0.8212 (p90) REVERT: K 60 MET cc_start: 0.9144 (tmm) cc_final: 0.8700 (tmm) REVERT: K 61 ILE cc_start: 0.9120 (mt) cc_final: 0.8557 (mt) REVERT: K 81 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8703 (mt-10) REVERT: K 153 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8707 (t70) REVERT: K 238 LEU cc_start: 0.9041 (mt) cc_final: 0.8733 (pp) REVERT: K 273 LYS cc_start: 0.9428 (tppt) cc_final: 0.8913 (mttm) REVERT: K 330 PHE cc_start: 0.9162 (m-80) cc_final: 0.8390 (m-80) REVERT: K 336 MET cc_start: 0.8882 (mmm) cc_final: 0.8460 (mmm) REVERT: K 369 ILE cc_start: 0.9381 (mt) cc_final: 0.8970 (mt) REVERT: K 406 SER cc_start: 0.9251 (m) cc_final: 0.9010 (p) REVERT: K 438 MET cc_start: 0.8880 (mmt) cc_final: 0.8429 (mmt) REVERT: K 447 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8193 (mt) REVERT: K 474 ARG cc_start: 0.3024 (mtt180) cc_final: 0.2551 (mtt180) REVERT: K 481 LEU cc_start: 0.8656 (tp) cc_final: 0.8302 (tp) REVERT: K 502 LYS cc_start: 0.9368 (mtpt) cc_final: 0.9047 (mtmm) REVERT: K 527 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8618 (mmmt) REVERT: K 538 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9070 (tp) REVERT: K 587 LYS cc_start: 0.9261 (mmtm) cc_final: 0.8756 (tppt) REVERT: K 588 MET cc_start: 0.9344 (mtm) cc_final: 0.8850 (mtp) REVERT: K 625 ILE cc_start: 0.9392 (mt) cc_final: 0.9002 (mm) REVERT: K 667 GLN cc_start: 0.9133 (pm20) cc_final: 0.8789 (pm20) REVERT: K 677 MET cc_start: 0.8908 (ttp) cc_final: 0.8621 (ttp) REVERT: K 727 ASP cc_start: 0.9499 (m-30) cc_final: 0.8888 (t0) REVERT: K 745 MET cc_start: 0.9097 (mpp) cc_final: 0.8716 (mtm) REVERT: M 5 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9263 (ptmm) REVERT: M 16 MET cc_start: 0.8726 (mmt) cc_final: 0.8354 (mmp) REVERT: M 62 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9359 (mm) REVERT: M 91 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8682 (mttm) REVERT: M 169 PHE cc_start: 0.9026 (m-10) cc_final: 0.8711 (m-80) REVERT: M 218 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8577 (mt) outliers start: 99 outliers final: 67 residues processed: 584 average time/residue: 0.3848 time to fit residues: 366.1223 Evaluate side-chains 562 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 485 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 153 HIS Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 99 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 321 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN L 174 ASN N 193 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.052873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044576 restraints weight = 143311.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046318 restraints weight = 72800.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047523 restraints weight = 45150.913| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29252 Z= 0.162 Angle : 0.680 14.696 39623 Z= 0.347 Chirality : 0.044 0.315 4524 Planarity : 0.004 0.057 4852 Dihedral : 13.308 178.633 4570 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.90 % Favored : 93.98 % Rotamer: Outliers : 3.24 % Allowed : 22.82 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3441 helix: 1.49 (0.14), residues: 1474 sheet: -0.08 (0.23), residues: 461 loop : -1.60 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 182 HIS 0.005 0.001 HIS M 146 PHE 0.028 0.001 PHE E 129 TYR 0.029 0.002 TYR K 62 ARG 0.004 0.000 ARG E 60 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1274) hydrogen bonds : angle 4.96972 ( 3747) SS BOND : bond 0.00381 ( 15) SS BOND : angle 1.83414 ( 30) covalent geometry : bond 0.00361 (29237) covalent geometry : angle 0.67854 (39593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 495 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8747 (m-30) cc_final: 0.8279 (t0) REVERT: A 42 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 56 PHE cc_start: 0.8944 (t80) cc_final: 0.8505 (t80) REVERT: A 60 ARG cc_start: 0.9287 (mmp80) cc_final: 0.8894 (mmm-85) REVERT: A 79 ILE cc_start: 0.9047 (mm) cc_final: 0.8751 (mp) REVERT: A 110 TYR cc_start: 0.9031 (t80) cc_final: 0.8817 (t80) REVERT: A 111 ASP cc_start: 0.9008 (t0) cc_final: 0.8660 (t0) REVERT: A 131 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8914 (mt-10) REVERT: B 22 ASP cc_start: 0.8849 (m-30) cc_final: 0.8196 (m-30) REVERT: B 26 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8479 (ptp90) REVERT: B 44 TYR cc_start: 0.9294 (t80) cc_final: 0.8910 (t80) REVERT: B 69 TYR cc_start: 0.8988 (t80) cc_final: 0.8604 (t80) REVERT: B 73 GLN cc_start: 0.9346 (tp40) cc_final: 0.9075 (tp-100) REVERT: B 78 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8222 (tp30) REVERT: B 90 SER cc_start: 0.9665 (m) cc_final: 0.9286 (p) REVERT: B 129 PHE cc_start: 0.8807 (t80) cc_final: 0.8425 (t80) REVERT: B 131 GLU cc_start: 0.9205 (mp0) cc_final: 0.8818 (pm20) REVERT: B 134 ASN cc_start: 0.9128 (m-40) cc_final: 0.8677 (m110) REVERT: C 44 TYR cc_start: 0.9132 (t80) cc_final: 0.8714 (t80) REVERT: C 45 VAL cc_start: 0.9525 (t) cc_final: 0.9180 (p) REVERT: C 71 MET cc_start: 0.9373 (mtm) cc_final: 0.9033 (mtm) REVERT: C 77 ASP cc_start: 0.9276 (t0) cc_final: 0.9055 (t0) REVERT: C 103 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9370 (tp) REVERT: C 134 ASN cc_start: 0.9731 (m-40) cc_final: 0.9414 (m110) REVERT: D 26 ARG cc_start: 0.9554 (mtm-85) cc_final: 0.9270 (ptp-110) REVERT: D 32 ILE cc_start: 0.9148 (tp) cc_final: 0.8934 (tp) REVERT: D 37 LYS cc_start: 0.9342 (tptt) cc_final: 0.9104 (tptp) REVERT: D 44 TYR cc_start: 0.9092 (t80) cc_final: 0.8742 (t80) REVERT: D 58 GLN cc_start: 0.9500 (mp-120) cc_final: 0.9268 (mm-40) REVERT: D 61 ARG cc_start: 0.9172 (mmm-85) cc_final: 0.8929 (mmm-85) REVERT: D 82 GLU cc_start: 0.9500 (tt0) cc_final: 0.9086 (tp30) REVERT: D 90 SER cc_start: 0.9506 (m) cc_final: 0.9295 (p) REVERT: D 95 GLU cc_start: 0.8425 (tp30) cc_final: 0.7991 (tm-30) REVERT: D 101 ASN cc_start: 0.9522 (m110) cc_final: 0.9217 (m-40) REVERT: D 131 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8911 (mt-10) REVERT: E 44 TYR cc_start: 0.9075 (t80) cc_final: 0.8825 (t80) REVERT: E 48 SER cc_start: 0.9703 (m) cc_final: 0.9450 (p) REVERT: E 55 SER cc_start: 0.9774 (m) cc_final: 0.9489 (p) REVERT: E 56 PHE cc_start: 0.9515 (t80) cc_final: 0.9226 (t80) REVERT: E 78 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8328 (mt-10) REVERT: E 82 GLU cc_start: 0.9352 (tm-30) cc_final: 0.9034 (tm-30) REVERT: E 101 ASN cc_start: 0.9532 (m110) cc_final: 0.9143 (m110) REVERT: E 105 TYR cc_start: 0.9284 (m-10) cc_final: 0.8848 (m-80) REVERT: E 110 TYR cc_start: 0.9461 (t80) cc_final: 0.9152 (t80) REVERT: E 114 THR cc_start: 0.9410 (m) cc_final: 0.9171 (p) REVERT: E 131 GLU cc_start: 0.9020 (tp30) cc_final: 0.8637 (tm-30) REVERT: E 135 ILE cc_start: 0.9603 (mm) cc_final: 0.9256 (mm) REVERT: J 46 MET cc_start: 0.8442 (mtt) cc_final: 0.7984 (mtt) REVERT: J 57 GLU cc_start: 0.8266 (mp0) cc_final: 0.7867 (tm-30) REVERT: J 99 MET cc_start: 0.9422 (ttp) cc_final: 0.9105 (ppp) REVERT: J 146 PHE cc_start: 0.9244 (m-80) cc_final: 0.8902 (m-80) REVERT: J 159 MET cc_start: 0.8979 (tpp) cc_final: 0.8680 (tpp) REVERT: J 209 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8535 (mp0) REVERT: J 229 MET cc_start: 0.8868 (tpp) cc_final: 0.8545 (tpp) REVERT: L 62 GLU cc_start: 0.8716 (tp30) cc_final: 0.8421 (mp0) REVERT: L 64 GLU cc_start: 0.9170 (mp0) cc_final: 0.8820 (mp0) REVERT: L 79 LYS cc_start: 0.9295 (mtpp) cc_final: 0.8696 (mtmm) REVERT: L 113 LYS cc_start: 0.9469 (ttmm) cc_final: 0.9242 (tppp) REVERT: L 115 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8722 (mm110) REVERT: L 118 LYS cc_start: 0.9595 (ttmm) cc_final: 0.9134 (ttmm) REVERT: N 49 MET cc_start: 0.9596 (tmm) cc_final: 0.9294 (tmm) REVERT: N 137 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7269 (p90) REVERT: N 155 MET cc_start: 0.9018 (pmm) cc_final: 0.8767 (pmm) REVERT: N 249 ARG cc_start: 0.9261 (ptm-80) cc_final: 0.8958 (ptm-80) REVERT: G 40 ASP cc_start: 0.9105 (m-30) cc_final: 0.8823 (p0) REVERT: G 66 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8975 (mt-10) REVERT: G 137 MET cc_start: 0.8965 (mpp) cc_final: 0.8262 (mpp) REVERT: F 33 GLN cc_start: 0.9432 (mp10) cc_final: 0.9013 (mp10) REVERT: F 73 ASN cc_start: 0.9528 (t0) cc_final: 0.9275 (t0) REVERT: F 137 MET cc_start: 0.8517 (ptp) cc_final: 0.8170 (mpp) REVERT: F 239 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9317 (mmmm) REVERT: H 5 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8720 (m) REVERT: H 19 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8105 (tm-30) REVERT: H 129 MET cc_start: 0.9292 (tpt) cc_final: 0.9045 (tpp) REVERT: H 145 TYR cc_start: 0.8607 (p90) cc_final: 0.8147 (p90) REVERT: H 174 ASP cc_start: 0.8709 (t0) cc_final: 0.8274 (t70) REVERT: H 200 MET cc_start: 0.9339 (tpp) cc_final: 0.9076 (tpp) REVERT: H 255 ASP cc_start: 0.9165 (m-30) cc_final: 0.8674 (p0) REVERT: H 266 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9105 (mp0) REVERT: I 99 ASP cc_start: 0.9531 (m-30) cc_final: 0.9170 (p0) REVERT: I 110 GLN cc_start: 0.9657 (tp40) cc_final: 0.9353 (tp40) REVERT: I 200 MET cc_start: 0.9087 (ttp) cc_final: 0.8270 (tmm) REVERT: I 275 TYR cc_start: 0.9018 (p90) cc_final: 0.8230 (p90) REVERT: K 60 MET cc_start: 0.9133 (tmm) cc_final: 0.8784 (tmm) REVERT: K 61 ILE cc_start: 0.9016 (mt) cc_final: 0.8591 (mt) REVERT: K 81 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8709 (mt-10) REVERT: K 148 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8972 (t) REVERT: K 153 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8576 (t70) REVERT: K 273 LYS cc_start: 0.9412 (tppt) cc_final: 0.8924 (mttm) REVERT: K 330 PHE cc_start: 0.9178 (m-80) cc_final: 0.8399 (m-80) REVERT: K 336 MET cc_start: 0.8877 (mmm) cc_final: 0.8427 (mmm) REVERT: K 369 ILE cc_start: 0.9410 (mt) cc_final: 0.8995 (mt) REVERT: K 406 SER cc_start: 0.9264 (m) cc_final: 0.9024 (p) REVERT: K 438 MET cc_start: 0.8901 (mmt) cc_final: 0.8440 (mmt) REVERT: K 447 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8202 (mt) REVERT: K 474 ARG cc_start: 0.3041 (mtt180) cc_final: 0.2557 (mtt180) REVERT: K 481 LEU cc_start: 0.8559 (tp) cc_final: 0.8228 (tp) REVERT: K 502 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9073 (mtmm) REVERT: K 527 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8642 (mmmt) REVERT: K 538 ILE cc_start: 0.9383 (tp) cc_final: 0.9065 (tp) REVERT: K 587 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8759 (tppt) REVERT: K 588 MET cc_start: 0.9356 (mtm) cc_final: 0.8854 (mtp) REVERT: K 625 ILE cc_start: 0.9369 (mt) cc_final: 0.8997 (mm) REVERT: K 667 GLN cc_start: 0.9139 (pm20) cc_final: 0.8796 (pm20) REVERT: K 677 MET cc_start: 0.8926 (ttp) cc_final: 0.8625 (ttp) REVERT: K 727 ASP cc_start: 0.9507 (m-30) cc_final: 0.8874 (t0) REVERT: K 730 GLU cc_start: 0.9075 (tt0) cc_final: 0.8743 (tp30) REVERT: K 745 MET cc_start: 0.9094 (mpp) cc_final: 0.8694 (mtm) REVERT: K 781 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9196 (mm) REVERT: M 5 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9269 (ptmm) REVERT: M 16 MET cc_start: 0.8737 (mmt) cc_final: 0.8369 (mmp) REVERT: M 62 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9364 (mm) REVERT: M 144 GLN cc_start: 0.8218 (tt0) cc_final: 0.7916 (tt0) REVERT: M 169 PHE cc_start: 0.9063 (m-10) cc_final: 0.8755 (m-80) outliers start: 100 outliers final: 80 residues processed: 567 average time/residue: 0.3955 time to fit residues: 369.4109 Evaluate side-chains 571 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 480 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 239 LYS Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 153 HIS Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 520 ASP Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 627 LEU Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain K residue 781 LEU Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 231 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.052606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044275 restraints weight = 143548.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046017 restraints weight = 73201.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047210 restraints weight = 45574.739| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29252 Z= 0.163 Angle : 0.690 14.790 39623 Z= 0.350 Chirality : 0.044 0.281 4524 Planarity : 0.004 0.058 4852 Dihedral : 13.321 178.507 4570 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 3.20 % Allowed : 22.94 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3441 helix: 1.46 (0.14), residues: 1474 sheet: -0.03 (0.23), residues: 454 loop : -1.57 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 182 HIS 0.004 0.001 HIS M 146 PHE 0.043 0.001 PHE K 245 TYR 0.034 0.002 TYR K 62 ARG 0.004 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 1274) hydrogen bonds : angle 4.97434 ( 3747) SS BOND : bond 0.00367 ( 15) SS BOND : angle 1.84875 ( 30) covalent geometry : bond 0.00361 (29237) covalent geometry : angle 0.68836 (39593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 493 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8729 (m-30) cc_final: 0.8236 (t0) REVERT: A 42 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 56 PHE cc_start: 0.8948 (t80) cc_final: 0.8472 (t80) REVERT: A 60 ARG cc_start: 0.9293 (mmp80) cc_final: 0.8912 (mmm-85) REVERT: A 71 MET cc_start: 0.9006 (mmm) cc_final: 0.8753 (mmt) REVERT: A 79 ILE cc_start: 0.9059 (mm) cc_final: 0.8765 (mp) REVERT: A 110 TYR cc_start: 0.9038 (t80) cc_final: 0.8818 (t80) REVERT: A 111 ASP cc_start: 0.9013 (t0) cc_final: 0.8666 (t0) REVERT: A 131 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8937 (mt-10) REVERT: B 22 ASP cc_start: 0.8845 (m-30) cc_final: 0.8183 (m-30) REVERT: B 26 ARG cc_start: 0.9144 (ptp-110) cc_final: 0.8468 (ptp90) REVERT: B 44 TYR cc_start: 0.9308 (t80) cc_final: 0.8934 (t80) REVERT: B 69 TYR cc_start: 0.8944 (t80) cc_final: 0.8565 (t80) REVERT: B 73 GLN cc_start: 0.9348 (tp40) cc_final: 0.9079 (tp-100) REVERT: B 78 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8216 (tp30) REVERT: B 90 SER cc_start: 0.9668 (m) cc_final: 0.9152 (p) REVERT: B 94 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8434 (mmm-85) REVERT: B 129 PHE cc_start: 0.8847 (t80) cc_final: 0.8585 (t80) REVERT: B 131 GLU cc_start: 0.9190 (mp0) cc_final: 0.8810 (pm20) REVERT: B 134 ASN cc_start: 0.9127 (m110) cc_final: 0.8691 (m110) REVERT: C 22 ASP cc_start: 0.9253 (m-30) cc_final: 0.8725 (p0) REVERT: C 44 TYR cc_start: 0.9138 (t80) cc_final: 0.8752 (t80) REVERT: C 45 VAL cc_start: 0.9530 (t) cc_final: 0.9183 (p) REVERT: C 71 MET cc_start: 0.9367 (mtm) cc_final: 0.9048 (mtm) REVERT: C 77 ASP cc_start: 0.9290 (t0) cc_final: 0.9070 (t0) REVERT: C 103 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9382 (tp) REVERT: C 105 TYR cc_start: 0.9344 (m-80) cc_final: 0.9059 (m-80) REVERT: C 134 ASN cc_start: 0.9737 (m-40) cc_final: 0.9418 (m110) REVERT: D 26 ARG cc_start: 0.9562 (mtm-85) cc_final: 0.9261 (ptp-110) REVERT: D 32 ILE cc_start: 0.9144 (tp) cc_final: 0.8936 (tp) REVERT: D 37 LYS cc_start: 0.9355 (tptt) cc_final: 0.9136 (tptp) REVERT: D 44 TYR cc_start: 0.9055 (t80) cc_final: 0.8764 (t80) REVERT: D 58 GLN cc_start: 0.9511 (mp-120) cc_final: 0.9168 (mm-40) REVERT: D 61 ARG cc_start: 0.9184 (mmm-85) cc_final: 0.8942 (mmm-85) REVERT: D 82 GLU cc_start: 0.9507 (tt0) cc_final: 0.9093 (tp30) REVERT: D 90 SER cc_start: 0.9512 (m) cc_final: 0.9298 (p) REVERT: D 101 ASN cc_start: 0.9507 (m110) cc_final: 0.9068 (m-40) REVERT: D 131 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8928 (mt-10) REVERT: E 44 TYR cc_start: 0.9079 (t80) cc_final: 0.8727 (t80) REVERT: E 55 SER cc_start: 0.9770 (m) cc_final: 0.9478 (p) REVERT: E 56 PHE cc_start: 0.9509 (t80) cc_final: 0.9208 (t80) REVERT: E 78 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8347 (mt-10) REVERT: E 82 GLU cc_start: 0.9355 (tm-30) cc_final: 0.9028 (tm-30) REVERT: E 101 ASN cc_start: 0.9539 (m110) cc_final: 0.9164 (m110) REVERT: E 105 TYR cc_start: 0.9290 (m-10) cc_final: 0.8881 (m-80) REVERT: E 110 TYR cc_start: 0.9495 (t80) cc_final: 0.9214 (t80) REVERT: E 131 GLU cc_start: 0.9053 (tp30) cc_final: 0.8615 (tm-30) REVERT: E 135 ILE cc_start: 0.9607 (mm) cc_final: 0.9256 (mm) REVERT: J 44 GLU cc_start: 0.8776 (pp20) cc_final: 0.7255 (pp20) REVERT: J 46 MET cc_start: 0.8426 (mtt) cc_final: 0.7968 (mmm) REVERT: J 99 MET cc_start: 0.9424 (ttp) cc_final: 0.9085 (ppp) REVERT: J 146 PHE cc_start: 0.9261 (m-80) cc_final: 0.8912 (m-80) REVERT: J 159 MET cc_start: 0.8985 (tpp) cc_final: 0.8689 (tpp) REVERT: J 166 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8648 (t) REVERT: J 209 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8532 (mp0) REVERT: L 43 MET cc_start: 0.8882 (ttp) cc_final: 0.8621 (tpp) REVERT: L 62 GLU cc_start: 0.8727 (tp30) cc_final: 0.8430 (mp0) REVERT: L 113 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9249 (tppp) REVERT: L 115 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8723 (mm110) REVERT: L 118 LYS cc_start: 0.9615 (ttmm) cc_final: 0.9186 (ttmm) REVERT: N 49 MET cc_start: 0.9594 (tmm) cc_final: 0.9287 (tmm) REVERT: N 137 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7273 (p90) REVERT: N 249 ARG cc_start: 0.9276 (ptm-80) cc_final: 0.8979 (ptm-80) REVERT: G 40 ASP cc_start: 0.9120 (m-30) cc_final: 0.8839 (p0) REVERT: G 66 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8967 (mt-10) REVERT: G 137 MET cc_start: 0.8959 (mpp) cc_final: 0.8294 (mpp) REVERT: F 33 GLN cc_start: 0.9429 (mp10) cc_final: 0.8997 (mp10) REVERT: F 73 ASN cc_start: 0.9534 (t0) cc_final: 0.9280 (t0) REVERT: F 137 MET cc_start: 0.8539 (ptp) cc_final: 0.8188 (mpp) REVERT: F 239 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9310 (mmmm) REVERT: H 5 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8726 (m) REVERT: H 19 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8067 (tm-30) REVERT: H 129 MET cc_start: 0.9299 (tpt) cc_final: 0.9052 (tpp) REVERT: H 145 TYR cc_start: 0.8672 (p90) cc_final: 0.8089 (p90) REVERT: H 174 ASP cc_start: 0.8734 (t0) cc_final: 0.8293 (t70) REVERT: H 200 MET cc_start: 0.9337 (tpp) cc_final: 0.9094 (tpp) REVERT: H 255 ASP cc_start: 0.9175 (m-30) cc_final: 0.8686 (p0) REVERT: I 99 ASP cc_start: 0.9538 (m-30) cc_final: 0.9150 (p0) REVERT: I 110 GLN cc_start: 0.9646 (tp40) cc_final: 0.9334 (tp40) REVERT: I 129 MET cc_start: 0.8813 (mmm) cc_final: 0.8393 (mmm) REVERT: I 200 MET cc_start: 0.9121 (ttp) cc_final: 0.8270 (tmm) REVERT: I 275 TYR cc_start: 0.9018 (p90) cc_final: 0.8242 (p90) REVERT: K 12 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9194 (mmmm) REVERT: K 60 MET cc_start: 0.9131 (tmm) cc_final: 0.8723 (tmm) REVERT: K 61 ILE cc_start: 0.8945 (mt) cc_final: 0.8417 (mt) REVERT: K 81 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8708 (mt-10) REVERT: K 148 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8977 (t) REVERT: K 273 LYS cc_start: 0.9411 (tppt) cc_final: 0.8917 (mttm) REVERT: K 330 PHE cc_start: 0.9153 (m-80) cc_final: 0.8280 (m-80) REVERT: K 336 MET cc_start: 0.8876 (mmm) cc_final: 0.8453 (mmm) REVERT: K 369 ILE cc_start: 0.9451 (mt) cc_final: 0.9016 (mm) REVERT: K 406 SER cc_start: 0.9270 (m) cc_final: 0.9040 (p) REVERT: K 438 MET cc_start: 0.8919 (mmt) cc_final: 0.8436 (mmt) REVERT: K 447 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8257 (mt) REVERT: K 474 ARG cc_start: 0.3042 (mtt180) cc_final: 0.2563 (mtt180) REVERT: K 481 LEU cc_start: 0.8560 (tp) cc_final: 0.8233 (tp) REVERT: K 502 LYS cc_start: 0.9378 (mtpt) cc_final: 0.9066 (mtmm) REVERT: K 527 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8706 (mmtt) REVERT: K 538 ILE cc_start: 0.9385 (tp) cc_final: 0.9069 (tp) REVERT: K 587 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8759 (tppt) REVERT: K 588 MET cc_start: 0.9361 (mtm) cc_final: 0.8871 (mtp) REVERT: K 625 ILE cc_start: 0.9373 (mt) cc_final: 0.9006 (mm) REVERT: K 677 MET cc_start: 0.8896 (ttp) cc_final: 0.8586 (ttp) REVERT: K 727 ASP cc_start: 0.9512 (m-30) cc_final: 0.8878 (t0) REVERT: K 730 GLU cc_start: 0.9083 (tt0) cc_final: 0.8749 (tp30) REVERT: K 745 MET cc_start: 0.9106 (mpp) cc_final: 0.8678 (mtm) REVERT: M 5 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9250 (ptmm) REVERT: M 16 MET cc_start: 0.8749 (mmt) cc_final: 0.8348 (mmp) REVERT: M 62 ILE cc_start: 0.9625 (OUTLIER) cc_final: 0.9359 (mm) REVERT: M 169 PHE cc_start: 0.9062 (m-10) cc_final: 0.8753 (m-80) outliers start: 99 outliers final: 79 residues processed: 565 average time/residue: 0.4186 time to fit residues: 387.0729 Evaluate side-chains 570 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 482 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 627 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 175 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.051823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043520 restraints weight = 145758.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045205 restraints weight = 74782.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046372 restraints weight = 46928.740| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29252 Z= 0.222 Angle : 0.731 14.800 39623 Z= 0.373 Chirality : 0.045 0.275 4524 Planarity : 0.004 0.057 4852 Dihedral : 13.390 179.312 4570 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 3.14 % Allowed : 23.33 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3441 helix: 1.38 (0.14), residues: 1474 sheet: -0.09 (0.23), residues: 460 loop : -1.57 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 182 HIS 0.006 0.001 HIS M 146 PHE 0.026 0.002 PHE E 56 TYR 0.040 0.002 TYR K 62 ARG 0.008 0.000 ARG K 244 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1274) hydrogen bonds : angle 5.12405 ( 3747) SS BOND : bond 0.00377 ( 15) SS BOND : angle 1.88263 ( 30) covalent geometry : bond 0.00479 (29237) covalent geometry : angle 0.72992 (39593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 476 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8732 (m-30) cc_final: 0.8249 (t0) REVERT: A 42 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 56 PHE cc_start: 0.8984 (t80) cc_final: 0.8511 (t80) REVERT: A 60 ARG cc_start: 0.9298 (mmp80) cc_final: 0.8934 (mmm-85) REVERT: A 71 MET cc_start: 0.9054 (mmm) cc_final: 0.8810 (mmt) REVERT: A 79 ILE cc_start: 0.9041 (mm) cc_final: 0.8739 (mp) REVERT: A 110 TYR cc_start: 0.9047 (t80) cc_final: 0.8771 (t80) REVERT: A 111 ASP cc_start: 0.9037 (t0) cc_final: 0.8679 (t0) REVERT: A 131 GLU cc_start: 0.9424 (mt-10) cc_final: 0.8978 (mt-10) REVERT: B 22 ASP cc_start: 0.8880 (m-30) cc_final: 0.8168 (m-30) REVERT: B 26 ARG cc_start: 0.9141 (ptp-110) cc_final: 0.8429 (ptp90) REVERT: B 69 TYR cc_start: 0.8987 (t80) cc_final: 0.8777 (t80) REVERT: B 73 GLN cc_start: 0.9360 (tp40) cc_final: 0.9083 (tp-100) REVERT: B 78 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8267 (tp30) REVERT: B 90 SER cc_start: 0.9659 (m) cc_final: 0.9273 (p) REVERT: B 129 PHE cc_start: 0.8850 (t80) cc_final: 0.8592 (t80) REVERT: B 131 GLU cc_start: 0.9182 (mp0) cc_final: 0.8794 (pm20) REVERT: B 134 ASN cc_start: 0.9112 (m110) cc_final: 0.8682 (m110) REVERT: C 44 TYR cc_start: 0.9197 (t80) cc_final: 0.8761 (t80) REVERT: C 71 MET cc_start: 0.9407 (mtm) cc_final: 0.9068 (mtm) REVERT: C 77 ASP cc_start: 0.9268 (t0) cc_final: 0.9026 (t0) REVERT: C 103 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9394 (tp) REVERT: C 105 TYR cc_start: 0.9351 (m-80) cc_final: 0.9066 (m-80) REVERT: C 134 ASN cc_start: 0.9753 (m-40) cc_final: 0.9439 (m110) REVERT: D 26 ARG cc_start: 0.9608 (mtm-85) cc_final: 0.9275 (ptp-110) REVERT: D 32 ILE cc_start: 0.9156 (tp) cc_final: 0.8932 (tp) REVERT: D 37 LYS cc_start: 0.9380 (tptt) cc_final: 0.9177 (tptp) REVERT: D 44 TYR cc_start: 0.8999 (t80) cc_final: 0.8785 (t80) REVERT: D 58 GLN cc_start: 0.9507 (mp-120) cc_final: 0.9164 (mm-40) REVERT: D 61 ARG cc_start: 0.9244 (mmm-85) cc_final: 0.8991 (mmm-85) REVERT: D 82 GLU cc_start: 0.9520 (tt0) cc_final: 0.9119 (tp30) REVERT: D 90 SER cc_start: 0.9518 (m) cc_final: 0.9304 (p) REVERT: D 101 ASN cc_start: 0.9434 (m110) cc_final: 0.9136 (m-40) REVERT: D 131 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8872 (mt-10) REVERT: E 19 ASP cc_start: 0.9233 (p0) cc_final: 0.9016 (p0) REVERT: E 44 TYR cc_start: 0.9116 (t80) cc_final: 0.8749 (t80) REVERT: E 55 SER cc_start: 0.9791 (m) cc_final: 0.9506 (p) REVERT: E 78 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8350 (mt-10) REVERT: E 79 ILE cc_start: 0.9440 (pt) cc_final: 0.9147 (pt) REVERT: E 82 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9049 (tm-30) REVERT: E 101 ASN cc_start: 0.9553 (m110) cc_final: 0.9152 (m110) REVERT: E 105 TYR cc_start: 0.9319 (m-10) cc_final: 0.8879 (m-80) REVERT: E 131 GLU cc_start: 0.9059 (tp30) cc_final: 0.8640 (tm-30) REVERT: E 135 ILE cc_start: 0.9629 (mm) cc_final: 0.9269 (mm) REVERT: J 44 GLU cc_start: 0.8797 (pp20) cc_final: 0.7317 (pp20) REVERT: J 46 MET cc_start: 0.8502 (mtt) cc_final: 0.8048 (mmm) REVERT: J 99 MET cc_start: 0.9476 (ttp) cc_final: 0.9091 (ppp) REVERT: J 146 PHE cc_start: 0.9276 (m-80) cc_final: 0.8919 (m-80) REVERT: J 159 MET cc_start: 0.8979 (tpp) cc_final: 0.8674 (tpp) REVERT: J 166 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8603 (t) REVERT: J 209 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8602 (mp0) REVERT: L 32 LEU cc_start: 0.8748 (tp) cc_final: 0.8547 (tp) REVERT: L 43 MET cc_start: 0.8897 (ttp) cc_final: 0.8629 (tpp) REVERT: L 62 GLU cc_start: 0.8623 (tp30) cc_final: 0.8405 (mp0) REVERT: L 113 LYS cc_start: 0.9500 (ttmm) cc_final: 0.9277 (tppp) REVERT: L 115 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8770 (mm110) REVERT: L 118 LYS cc_start: 0.9629 (ttmm) cc_final: 0.9211 (ttmm) REVERT: N 49 MET cc_start: 0.9613 (tmm) cc_final: 0.9279 (tmm) REVERT: N 137 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7266 (p90) REVERT: N 249 ARG cc_start: 0.9321 (ptm-80) cc_final: 0.9059 (ptm-80) REVERT: G 40 ASP cc_start: 0.9163 (m-30) cc_final: 0.8859 (p0) REVERT: G 66 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8962 (mt-10) REVERT: G 137 MET cc_start: 0.8944 (mpp) cc_final: 0.8339 (mpp) REVERT: G 147 GLN cc_start: 0.7852 (pm20) cc_final: 0.6520 (pm20) REVERT: F 33 GLN cc_start: 0.9433 (mp10) cc_final: 0.8986 (mp10) REVERT: F 73 ASN cc_start: 0.9573 (t0) cc_final: 0.9325 (t0) REVERT: F 137 MET cc_start: 0.8635 (ptp) cc_final: 0.8267 (mpp) REVERT: F 239 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9274 (mmmm) REVERT: H 5 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8739 (m) REVERT: H 19 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8094 (tm-30) REVERT: H 145 TYR cc_start: 0.8740 (p90) cc_final: 0.8281 (p90) REVERT: H 174 ASP cc_start: 0.8829 (t0) cc_final: 0.8379 (t70) REVERT: H 200 MET cc_start: 0.9371 (tpp) cc_final: 0.9114 (tpp) REVERT: H 255 ASP cc_start: 0.9215 (m-30) cc_final: 0.8777 (p0) REVERT: H 261 MET cc_start: 0.9155 (mmm) cc_final: 0.8839 (mmm) REVERT: I 99 ASP cc_start: 0.9576 (m-30) cc_final: 0.9201 (p0) REVERT: I 110 GLN cc_start: 0.9657 (tp40) cc_final: 0.9371 (tp40) REVERT: I 200 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8679 (ttp) REVERT: I 265 MET cc_start: 0.9682 (mtm) cc_final: 0.9479 (mtm) REVERT: I 275 TYR cc_start: 0.9076 (p90) cc_final: 0.8315 (p90) REVERT: K 60 MET cc_start: 0.9168 (tmm) cc_final: 0.8759 (tmm) REVERT: K 61 ILE cc_start: 0.8970 (mt) cc_final: 0.8432 (mt) REVERT: K 81 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8604 (mt-10) REVERT: K 148 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8957 (t) REVERT: K 330 PHE cc_start: 0.9129 (m-80) cc_final: 0.8275 (m-80) REVERT: K 336 MET cc_start: 0.8911 (mmm) cc_final: 0.8476 (mmm) REVERT: K 369 ILE cc_start: 0.9493 (mt) cc_final: 0.9081 (mm) REVERT: K 406 SER cc_start: 0.9293 (m) cc_final: 0.9069 (p) REVERT: K 438 MET cc_start: 0.8926 (mmt) cc_final: 0.8441 (mmt) REVERT: K 447 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8060 (mt) REVERT: K 474 ARG cc_start: 0.2953 (mtt180) cc_final: 0.2459 (mtt180) REVERT: K 481 LEU cc_start: 0.8654 (tp) cc_final: 0.8333 (tp) REVERT: K 502 LYS cc_start: 0.9419 (mtpt) cc_final: 0.9110 (mtmm) REVERT: K 527 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8666 (mmtt) REVERT: K 538 ILE cc_start: 0.9385 (tp) cc_final: 0.9087 (tp) REVERT: K 587 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8832 (tppt) REVERT: K 588 MET cc_start: 0.9370 (mtm) cc_final: 0.8876 (mtp) REVERT: K 625 ILE cc_start: 0.9371 (mt) cc_final: 0.8969 (mm) REVERT: K 727 ASP cc_start: 0.9528 (m-30) cc_final: 0.8863 (t0) REVERT: K 730 GLU cc_start: 0.9084 (tt0) cc_final: 0.8754 (tp30) REVERT: K 745 MET cc_start: 0.9067 (mpp) cc_final: 0.8656 (mtm) REVERT: M 5 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9208 (ptmm) REVERT: M 16 MET cc_start: 0.8699 (mmt) cc_final: 0.8387 (mmp) REVERT: M 62 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9392 (mm) REVERT: M 82 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8868 (tp) REVERT: M 169 PHE cc_start: 0.9055 (m-10) cc_final: 0.8847 (m-80) outliers start: 97 outliers final: 76 residues processed: 544 average time/residue: 0.3932 time to fit residues: 347.7459 Evaluate side-chains 557 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 470 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 627 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 15 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.052710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044362 restraints weight = 143188.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046098 restraints weight = 73092.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047279 restraints weight = 45522.406| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29252 Z= 0.157 Angle : 0.712 15.120 39623 Z= 0.361 Chirality : 0.045 0.274 4524 Planarity : 0.004 0.057 4852 Dihedral : 13.365 178.358 4570 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 3.17 % Allowed : 23.59 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3441 helix: 1.40 (0.14), residues: 1474 sheet: -0.02 (0.23), residues: 460 loop : -1.54 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 182 HIS 0.005 0.001 HIS G 230 PHE 0.032 0.001 PHE K 245 TYR 0.033 0.002 TYR K 62 ARG 0.012 0.000 ARG K 244 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1274) hydrogen bonds : angle 5.02778 ( 3747) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.79808 ( 30) covalent geometry : bond 0.00349 (29237) covalent geometry : angle 0.71037 (39593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10661.50 seconds wall clock time: 185 minutes 40.20 seconds (11140.20 seconds total)