Starting phenix.real_space_refine on Sat Sep 28 14:25:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/09_2024/6xn4_22267.cif" } resolution = 3.35 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= 0.003 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 64 5.49 5 S 48 5.16 5 C 12041 2.51 5 N 3263 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2227 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2272 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 736 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 25} Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Time building chain proxies: 12.22, per 1000 atoms: 0.63 Number of scatterers: 19273 At special positions: 0 Unit cell: (109.548, 126.732, 183.654, 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 48 16.00 P 64 15.00 O 3857 8.00 N 3263 7.00 C 12041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 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: 4.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 40.5% alpha, 12.8% beta 2 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.582A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.555A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.073A pdb=" N LEU B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.543A pdb=" N LEU F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLY F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.546A pdb=" N ARG F 183 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 157 through 174 removed outlier: 3.537A pdb=" N ASN H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.797A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.539A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.732A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 73 removed outlier: 4.369A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.554A pdb=" N ALA D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.621A pdb=" N THR D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.506A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.657A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.300A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.116A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.801A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.522A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.848A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 224 removed outlier: 3.597A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 270 through 295 removed outlier: 4.081A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 364 through 381 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.878A pdb=" N SER A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.931A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.679A pdb=" N GLU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.920A pdb=" N THR A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.391A pdb=" N ASP A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.710A pdb=" N ASP A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.522A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.654A pdb=" N GLY A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.574A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.514A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 65 removed outlier: 3.803A pdb=" N VAL J 62 " --> pdb=" O PHE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.684A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.637A pdb=" N ALA J 154 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 229 removed outlier: 3.650A pdb=" N ILE J 213 " --> pdb=" O THR J 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP J 228 " --> pdb=" O TYR J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 removed outlier: 4.047A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 292 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.649A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.858A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 96 removed outlier: 7.675A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AA9, first strand: chain 'H' and resid 94 through 95 removed outlier: 3.723A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 94 through 95 removed outlier: 6.447A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.804A pdb=" N PHE C 42 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 304 through 305 removed outlier: 4.215A pdb=" N PHE A 247 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 352 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 249 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AC1, first strand: chain 'A' and resid 568 through 570 removed outlier: 3.518A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AC3, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC4, first strand: chain 'J' and resid 22 through 23 removed outlier: 6.666A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN J 173 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 37 through 40 removed outlier: 3.897A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 314 through 315 729 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6115 1.34 - 1.48: 5333 1.48 - 1.62: 8202 1.62 - 1.76: 4 1.76 - 1.89: 88 Bond restraints: 19742 Sorted by residual: bond pdb=" CA ASN J 141 " pdb=" C ASN J 141 " ideal model delta sigma weight residual 1.522 1.436 0.087 1.37e-02 5.33e+03 4.00e+01 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.15e-02 7.56e+03 1.28e+01 bond pdb=" C LYS J 170 " pdb=" N VAL J 171 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.46e-02 4.69e+03 7.61e+00 bond pdb=" CG1 ILE A 708 " pdb=" CD1 ILE A 708 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.45e+00 bond pdb=" C GLN J 259 " pdb=" N PRO J 260 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 19737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 26473 4.07 - 8.15: 381 8.15 - 12.22: 30 12.22 - 16.30: 3 16.30 - 20.37: 1 Bond angle restraints: 26888 Sorted by residual: angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.77 -20.37 2.30e+00 1.89e-01 7.84e+01 angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 123.91 136.92 -13.01 1.66e+00 3.63e-01 6.14e+01 angle pdb=" N ILE J 17 " pdb=" CA ILE J 17 " pdb=" C ILE J 17 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 107.52 6.19 9.50e-01 1.11e+00 4.24e+01 angle pdb=" N VAL A 199 " pdb=" CA VAL A 199 " pdb=" C VAL A 199 " ideal model delta sigma weight residual 113.10 107.33 5.77 9.70e-01 1.06e+00 3.54e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 11568 34.63 - 69.25: 374 69.25 - 103.88: 38 103.88 - 138.50: 4 138.50 - 173.13: 2 Dihedral angle restraints: 11986 sinusoidal: 5486 harmonic: 6500 Sorted by residual: dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual 180.00 46.16 133.84 0 5.00e+00 4.00e-02 7.16e+02 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual 180.00 116.21 63.79 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ILE G 26 " pdb=" C ILE G 26 " pdb=" N GLY G 27 " pdb=" CA GLY G 27 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2711 0.100 - 0.200: 299 0.200 - 0.300: 33 0.300 - 0.399: 4 0.399 - 0.499: 3 Chirality restraints: 3050 Sorted by residual: chirality pdb=" CB ILE A 708 " pdb=" CA ILE A 708 " pdb=" CG1 ILE A 708 " pdb=" CG2 ILE A 708 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1' A T 29 " pdb=" O4' A T 29 " pdb=" C2' A T 29 " pdb=" N9 A T 29 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3047 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 15 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C MET H 15 " 0.065 2.00e-02 2.50e+03 pdb=" O MET H 15 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS H 16 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 137 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU C 137 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 137 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 15 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET G 15 " 0.056 2.00e-02 2.50e+03 pdb=" O MET G 15 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS G 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1373 2.71 - 3.26: 19283 3.26 - 3.81: 34177 3.81 - 4.35: 41684 4.35 - 4.90: 68043 Nonbonded interactions: 164560 Sorted by model distance: nonbonded pdb=" OG SER B 128 " pdb=" OH TYR B 186 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" O TYR A 383 " model vdw 2.200 3.040 nonbonded pdb=" OG SER F 47 " pdb=" OP1 A R 9 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OP2 U T 22 " model vdw 2.240 3.040 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.243 3.040 ... (remaining 164555 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 'C' and resid 12 through 146) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 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: 0.000 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 49.340 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.009 0.106 19742 Z= 0.572 Angle : 1.238 20.371 26888 Z= 0.678 Chirality : 0.067 0.499 3050 Planarity : 0.006 0.052 3212 Dihedral : 17.199 173.125 7793 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -3.52 (0.15), residues: 2202 helix: -2.11 (0.15), residues: 827 sheet: -1.71 (0.27), residues: 323 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 186 HIS 0.009 0.002 HIS J 282 PHE 0.049 0.004 PHE J 255 TYR 0.036 0.004 TYR J 283 ARG 0.020 0.001 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: F 120 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6603 (mm-30) REVERT: H 55 TYR cc_start: 0.8762 (t80) cc_final: 0.8487 (t80) REVERT: A 86 MET cc_start: 0.2028 (mpp) cc_final: 0.1611 (mpp) REVERT: A 250 MET cc_start: 0.8612 (tmm) cc_final: 0.8124 (tmm) REVERT: A 447 MET cc_start: 0.8166 (ptt) cc_final: 0.7550 (ptt) REVERT: A 453 MET cc_start: 0.8017 (ttm) cc_final: 0.7631 (ttm) REVERT: A 580 MET cc_start: 0.7654 (mtm) cc_final: 0.7385 (mtm) REVERT: J 292 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7938 (tpp80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2903 time to fit residues: 51.1410 Evaluate side-chains 81 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 131 optimal weight: 40.0000 chunk 204 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 124 ASN H 192 ASN A 251 ASN A 355 ASN J 74 ASN J 92 GLN J 111 ASN J 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19742 Z= 0.197 Angle : 0.678 16.334 26888 Z= 0.361 Chirality : 0.043 0.224 3050 Planarity : 0.004 0.054 3212 Dihedral : 16.326 159.880 3392 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.69 % Rotamer: Outliers : 0.57 % Allowed : 6.92 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.70 (0.16), residues: 2202 helix: -0.97 (0.16), residues: 849 sheet: -1.58 (0.24), residues: 384 loop : -2.61 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 334 HIS 0.004 0.001 HIS H 16 PHE 0.039 0.001 PHE A 36 TYR 0.018 0.002 TYR B 232 ARG 0.005 0.001 ARG J 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8583 (tt) cc_final: 0.8337 (tt) REVERT: F 1 MET cc_start: 0.7588 (tpp) cc_final: 0.7369 (tpp) REVERT: F 120 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6424 (mm-30) REVERT: A 86 MET cc_start: 0.2161 (mpp) cc_final: 0.1767 (mpp) REVERT: A 250 MET cc_start: 0.8587 (tmm) cc_final: 0.8067 (tmm) REVERT: A 447 MET cc_start: 0.8053 (ptt) cc_final: 0.7737 (ptp) REVERT: A 453 MET cc_start: 0.8314 (ttm) cc_final: 0.8011 (ttt) REVERT: A 580 MET cc_start: 0.7765 (mtm) cc_final: 0.7546 (mtm) REVERT: J 292 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7902 (tpp80) outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 0.3108 time to fit residues: 57.6965 Evaluate side-chains 88 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 139 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS A 355 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19742 Z= 0.200 Angle : 0.623 15.670 26888 Z= 0.333 Chirality : 0.043 0.222 3050 Planarity : 0.004 0.053 3212 Dihedral : 16.009 162.606 3392 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.95 % Favored : 91.92 % Rotamer: Outliers : 0.77 % Allowed : 10.94 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.19 (0.17), residues: 2202 helix: -0.34 (0.17), residues: 845 sheet: -1.43 (0.25), residues: 374 loop : -2.47 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 186 HIS 0.004 0.001 HIS H 16 PHE 0.024 0.001 PHE A 36 TYR 0.019 0.002 TYR A 77 ARG 0.006 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8626 (tt) cc_final: 0.8391 (tt) REVERT: F 6 GLU cc_start: 0.7600 (tp30) cc_final: 0.7255 (tp30) REVERT: F 120 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6467 (mm-30) REVERT: G 53 MET cc_start: 0.8808 (mtp) cc_final: 0.8582 (ttt) REVERT: A 250 MET cc_start: 0.8670 (tmm) cc_final: 0.8095 (tmm) REVERT: A 447 MET cc_start: 0.7982 (ptt) cc_final: 0.7588 (ptp) REVERT: A 453 MET cc_start: 0.8359 (ttm) cc_final: 0.8067 (ttt) REVERT: A 580 MET cc_start: 0.7721 (mtm) cc_final: 0.7391 (mtm) REVERT: J 292 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7610 (tpp80) outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.2658 time to fit residues: 47.0831 Evaluate side-chains 92 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN F 16 HIS F 121 ASN F 131 ASN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 19742 Z= 0.535 Angle : 0.835 17.167 26888 Z= 0.440 Chirality : 0.049 0.323 3050 Planarity : 0.005 0.062 3212 Dihedral : 16.704 163.792 3392 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.26 % Favored : 89.60 % Rotamer: Outliers : 1.96 % Allowed : 13.16 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.35 (0.17), residues: 2202 helix: -0.38 (0.17), residues: 848 sheet: -1.66 (0.26), residues: 356 loop : -2.58 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.008 0.002 HIS J 282 PHE 0.028 0.002 PHE G 96 TYR 0.025 0.003 TYR B 186 ARG 0.007 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 83 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: B 94 LYS cc_start: 0.8239 (pttm) cc_final: 0.7561 (ttpt) REVERT: B 194 LEU cc_start: 0.8685 (tt) cc_final: 0.8477 (tt) REVERT: C 39 HIS cc_start: 0.7698 (m90) cc_final: 0.7142 (m90) REVERT: C 62 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 106 ASP cc_start: 0.7177 (p0) cc_final: 0.6927 (p0) REVERT: C 109 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7471 (tm-30) REVERT: A 250 MET cc_start: 0.8636 (tmm) cc_final: 0.8022 (tmm) REVERT: A 580 MET cc_start: 0.7698 (mtm) cc_final: 0.7344 (mtm) REVERT: A 731 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8909 (mt-10) outliers start: 38 outliers final: 18 residues processed: 115 average time/residue: 0.2631 time to fit residues: 52.1562 Evaluate side-chains 96 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19742 Z= 0.173 Angle : 0.614 15.115 26888 Z= 0.325 Chirality : 0.042 0.213 3050 Planarity : 0.003 0.057 3212 Dihedral : 15.950 156.773 3392 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.67 % Favored : 92.19 % Rotamer: Outliers : 1.50 % Allowed : 14.30 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.02 (0.17), residues: 2202 helix: 0.01 (0.18), residues: 847 sheet: -1.55 (0.26), residues: 348 loop : -2.47 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 186 HIS 0.003 0.001 HIS A 55 PHE 0.014 0.001 PHE A 36 TYR 0.015 0.001 TYR J 28 ARG 0.006 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8673 (tt) cc_final: 0.8445 (tt) REVERT: C 39 HIS cc_start: 0.7732 (m90) cc_final: 0.7404 (m90) REVERT: C 62 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 106 ASP cc_start: 0.7142 (p0) cc_final: 0.6889 (p0) REVERT: C 109 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7442 (tm-30) REVERT: A 142 PRO cc_start: 0.4799 (Cg_exo) cc_final: 0.4539 (Cg_endo) REVERT: A 250 MET cc_start: 0.8640 (tmm) cc_final: 0.8116 (tmm) REVERT: A 580 MET cc_start: 0.7772 (mtm) cc_final: 0.7493 (mtm) REVERT: A 731 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8872 (mp0) outliers start: 29 outliers final: 15 residues processed: 113 average time/residue: 0.2897 time to fit residues: 56.1869 Evaluate side-chains 98 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19742 Z= 0.283 Angle : 0.648 15.482 26888 Z= 0.342 Chirality : 0.044 0.246 3050 Planarity : 0.004 0.053 3212 Dihedral : 16.068 160.752 3392 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.67 % Favored : 91.14 % Rotamer: Outliers : 1.81 % Allowed : 14.97 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.95 (0.17), residues: 2202 helix: 0.07 (0.18), residues: 849 sheet: -1.51 (0.25), residues: 352 loop : -2.45 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 186 HIS 0.004 0.001 HIS H 16 PHE 0.015 0.002 PHE F 162 TYR 0.015 0.002 TYR C 89 ARG 0.004 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8685 (tt) cc_final: 0.8479 (tt) REVERT: F 106 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: H 8 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8225 (p) REVERT: H 121 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7194 (p0) REVERT: G 167 GLN cc_start: 0.7684 (pt0) cc_final: 0.7364 (tm-30) REVERT: C 39 HIS cc_start: 0.7798 (m90) cc_final: 0.7296 (m-70) REVERT: C 62 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 109 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7500 (tm-30) REVERT: A 142 PRO cc_start: 0.4792 (Cg_exo) cc_final: 0.4547 (Cg_endo) REVERT: A 250 MET cc_start: 0.8633 (tmm) cc_final: 0.8016 (tmm) REVERT: A 580 MET cc_start: 0.7711 (mtm) cc_final: 0.7402 (mtm) REVERT: A 731 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8786 (mp0) REVERT: J 289 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8245 (p0) outliers start: 35 outliers final: 20 residues processed: 112 average time/residue: 0.2632 time to fit residues: 50.1916 Evaluate side-chains 108 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 289 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 135 optimal weight: 0.0020 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 ASN J 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19742 Z= 0.167 Angle : 0.590 15.032 26888 Z= 0.310 Chirality : 0.041 0.196 3050 Planarity : 0.003 0.051 3212 Dihedral : 15.695 158.100 3392 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 1.50 % Allowed : 16.21 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.79 (0.17), residues: 2202 helix: 0.22 (0.18), residues: 854 sheet: -1.44 (0.26), residues: 338 loop : -2.37 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 186 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE J 255 TYR 0.012 0.001 TYR A 77 ARG 0.005 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8686 (tt) cc_final: 0.8453 (tt) REVERT: F 106 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: H 120 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: G 167 GLN cc_start: 0.7509 (pt0) cc_final: 0.7157 (tm-30) REVERT: C 39 HIS cc_start: 0.7877 (m90) cc_final: 0.7253 (m90) REVERT: C 62 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: C 106 ASP cc_start: 0.7156 (p0) cc_final: 0.6898 (p0) REVERT: C 109 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7513 (tm-30) REVERT: A 75 ILE cc_start: 0.7619 (mm) cc_final: 0.7050 (mt) REVERT: A 142 PRO cc_start: 0.4735 (Cg_exo) cc_final: 0.4496 (Cg_endo) REVERT: A 250 MET cc_start: 0.8667 (tmm) cc_final: 0.8049 (tmm) REVERT: A 447 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7625 (ptp) REVERT: A 580 MET cc_start: 0.7762 (mtm) cc_final: 0.7483 (mtm) outliers start: 29 outliers final: 20 residues processed: 115 average time/residue: 0.2885 time to fit residues: 56.8737 Evaluate side-chains 110 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 50.0000 chunk 147 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN H 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 19742 Z= 0.473 Angle : 0.781 16.437 26888 Z= 0.408 Chirality : 0.048 0.293 3050 Planarity : 0.005 0.055 3212 Dihedral : 16.423 162.689 3392 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.99 % Favored : 89.87 % Rotamer: Outliers : 2.27 % Allowed : 15.95 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.09 (0.17), residues: 2202 helix: -0.06 (0.17), residues: 853 sheet: -1.62 (0.26), residues: 348 loop : -2.51 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.006 0.002 HIS J 155 PHE 0.023 0.002 PHE G 96 TYR 0.022 0.002 TYR B 186 ARG 0.007 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 84 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.8482 (ptt) cc_final: 0.8188 (ptt) REVERT: B 94 LYS cc_start: 0.8238 (pttm) cc_final: 0.7610 (mtpt) REVERT: F 106 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8529 (pp20) REVERT: H 121 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.6892 (p0) REVERT: G 167 GLN cc_start: 0.7744 (pt0) cc_final: 0.7414 (tm-30) REVERT: C 39 HIS cc_start: 0.7795 (m90) cc_final: 0.7296 (m90) REVERT: C 106 ASP cc_start: 0.7394 (p0) cc_final: 0.7088 (p0) REVERT: C 109 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7619 (tm-30) REVERT: A 142 PRO cc_start: 0.4847 (Cg_exo) cc_final: 0.4607 (Cg_endo) REVERT: A 250 MET cc_start: 0.8632 (tmm) cc_final: 0.7973 (tmm) REVERT: A 580 MET cc_start: 0.7636 (mtm) cc_final: 0.7293 (mtm) outliers start: 44 outliers final: 30 residues processed: 121 average time/residue: 0.2493 time to fit residues: 51.6982 Evaluate side-chains 108 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 0.0060 chunk 121 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19742 Z= 0.209 Angle : 0.638 15.311 26888 Z= 0.331 Chirality : 0.043 0.228 3050 Planarity : 0.003 0.049 3212 Dihedral : 15.898 159.256 3392 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 1.55 % Allowed : 16.73 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.86 (0.17), residues: 2202 helix: 0.18 (0.18), residues: 849 sheet: -1.53 (0.26), residues: 342 loop : -2.40 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.004 0.001 HIS J 155 PHE 0.013 0.001 PHE H 119 TYR 0.014 0.001 TYR F 55 ARG 0.004 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 2.201 Fit side-chains revert: symmetry clash REVERT: B 76 MET cc_start: 0.7776 (ptt) cc_final: 0.7380 (ptt) REVERT: F 106 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8540 (pp20) REVERT: H 120 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: H 121 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6744 (p0) REVERT: G 167 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: C 39 HIS cc_start: 0.7792 (m90) cc_final: 0.7193 (m90) REVERT: C 62 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: C 106 ASP cc_start: 0.7109 (p0) cc_final: 0.6797 (p0) REVERT: C 109 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7607 (tm-30) REVERT: A 142 PRO cc_start: 0.5082 (Cg_exo) cc_final: 0.4839 (Cg_endo) REVERT: A 250 MET cc_start: 0.8625 (tmm) cc_final: 0.7992 (tmm) REVERT: A 491 MET cc_start: 0.6043 (ptt) cc_final: 0.5787 (ppp) REVERT: A 580 MET cc_start: 0.7673 (mtm) cc_final: 0.7465 (mtm) REVERT: J 289 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8185 (p0) outliers start: 30 outliers final: 20 residues processed: 109 average time/residue: 0.2819 time to fit residues: 52.0781 Evaluate side-chains 107 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19742 Z= 0.272 Angle : 0.663 15.379 26888 Z= 0.344 Chirality : 0.043 0.237 3050 Planarity : 0.004 0.049 3212 Dihedral : 15.955 160.016 3392 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.99 % Favored : 90.87 % Rotamer: Outliers : 1.60 % Allowed : 16.52 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.86 (0.17), residues: 2202 helix: 0.19 (0.18), residues: 849 sheet: -1.59 (0.25), residues: 358 loop : -2.39 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 186 HIS 0.004 0.001 HIS J 155 PHE 0.014 0.001 PHE F 162 TYR 0.014 0.002 TYR F 55 ARG 0.004 0.000 ARG D 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 2.216 Fit side-chains revert: symmetry clash REVERT: B 76 MET cc_start: 0.8234 (ptt) cc_final: 0.7861 (ptt) REVERT: F 106 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8534 (pp20) REVERT: H 120 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: G 167 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: C 39 HIS cc_start: 0.7829 (m90) cc_final: 0.7243 (m90) REVERT: C 62 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 106 ASP cc_start: 0.7096 (p0) cc_final: 0.6783 (p0) REVERT: C 109 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7621 (tm-30) REVERT: A 142 PRO cc_start: 0.5092 (Cg_exo) cc_final: 0.4848 (Cg_endo) REVERT: A 250 MET cc_start: 0.8636 (tmm) cc_final: 0.8000 (tmm) REVERT: A 491 MET cc_start: 0.6035 (ptt) cc_final: 0.5787 (ppp) REVERT: A 580 MET cc_start: 0.7700 (mtm) cc_final: 0.7466 (mtm) REVERT: J 289 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8191 (p0) outliers start: 31 outliers final: 25 residues processed: 106 average time/residue: 0.2632 time to fit residues: 47.8372 Evaluate side-chains 109 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 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 = 0.3956 r_free = 0.3956 target = 0.079114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061679 restraints weight = 94701.473| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.52 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19742 Z= 0.338 Angle : 0.703 15.824 26888 Z= 0.365 Chirality : 0.045 0.264 3050 Planarity : 0.004 0.048 3212 Dihedral : 16.124 161.480 3392 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.63 % Favored : 90.24 % Rotamer: Outliers : 1.91 % Allowed : 16.57 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.90 (0.17), residues: 2202 helix: 0.12 (0.18), residues: 849 sheet: -1.58 (0.26), residues: 338 loop : -2.38 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.005 0.001 HIS J 155 PHE 0.017 0.002 PHE D 129 TYR 0.016 0.002 TYR J 283 ARG 0.005 0.000 ARG D 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.20 seconds wall clock time: 66 minutes 56.98 seconds (4016.98 seconds total)