Starting phenix.real_space_refine on Tue Jun 24 04:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5s_14336/06_2025/7r5s_14336.cif" } resolution = 2.83 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1895 atoms to isotropic. 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 82 5.49 5 S 139 5.16 5 C 16926 2.51 5 N 4596 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5014 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 849 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "K" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1922 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2502 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2613 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1365 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "W" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "i" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 15.70, per 1000 atoms: 0.58 Number of scatterers: 26871 At special positions: 0 Unit cell: (136.48, 203.014, 196.19, 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 139 16.00 P 82 15.00 O 5128 8.00 N 4596 7.00 C 16926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.66 Conformation dependent library (CDL) restraints added in 3.5 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 15 sheets defined 64.6% alpha, 9.6% beta 37 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 removed outlier: 3.895A pdb=" N ARG H 39 " --> pdb=" O CYS H 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 114 removed outlier: 4.300A pdb=" N ALA H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.935A pdb=" N GLN H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 188 removed outlier: 3.906A pdb=" N LYS H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER H 170 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP H 185 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU H 186 " --> pdb=" O GLN H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.339A pdb=" N GLN H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN H 201 " --> pdb=" O ILE H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.811A pdb=" N ILE H 236 " --> pdb=" O ALA H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.620A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.608A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY I 119 " --> pdb=" O ILE I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 4.681A pdb=" N ARG I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 154 removed outlier: 3.871A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY I 154 " --> pdb=" O TRP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.627A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 194 removed outlier: 3.612A pdb=" N ASP I 194 " --> pdb=" O SER I 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 194' Processing helix chain 'I' and resid 197 through 209 removed outlier: 3.538A pdb=" N LEU I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.825A pdb=" N LEU I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 281 Processing helix chain 'I' and resid 328 through 333 removed outlier: 3.605A pdb=" N CYS I 332 " --> pdb=" O SER I 328 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 333' Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.673A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 377 removed outlier: 3.590A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 400 Processing helix chain 'I' and resid 411 through 427 removed outlier: 3.727A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 430 No H-bonds generated for 'chain 'I' and resid 428 through 430' Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.637A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.519A pdb=" N SER I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 483 Proline residue: I 472 - end of helix removed outlier: 4.927A pdb=" N ASP I 476 " --> pdb=" O PRO I 472 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 510 removed outlier: 3.906A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 514 Processing helix chain 'I' and resid 525 through 551 removed outlier: 3.750A pdb=" N ASN I 531 " --> pdb=" O GLY I 527 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.963A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 575 Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.578A pdb=" N LEU I 593 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 625 removed outlier: 3.708A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS I 619 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 652 removed outlier: 3.961A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 removed outlier: 4.219A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 697 Processing helix chain 'I' and resid 719 through 727 removed outlier: 3.558A pdb=" N GLY I 727 " --> pdb=" O LEU I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 740 removed outlier: 3.545A pdb=" N HIS I 740 " --> pdb=" O ARG I 736 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 55 through 76 removed outlier: 3.610A pdb=" N SER K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 149 removed outlier: 3.975A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 188 Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.514A pdb=" N MET K 215 " --> pdb=" O THR K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 Processing helix chain 'L' and resid 27 through 37 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 88 through 104 Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.806A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.591A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 227 Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.627A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.736A pdb=" N LEU L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 removed outlier: 3.543A pdb=" N THR L 302 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.697A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 37 Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.934A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.844A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.875A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.706A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.615A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 36 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 4.184A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 3.770A pdb=" N LEU N 112 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.681A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 160 through 169 removed outlier: 3.961A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.969A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.568A pdb=" N VAL O 283 " --> pdb=" O PRO O 279 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 removed outlier: 3.746A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 removed outlier: 3.611A pdb=" N HIS P 186 " --> pdb=" O ARG P 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.919A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.820A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 124 removed outlier: 3.919A pdb=" N ILE Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 197 removed outlier: 3.881A pdb=" N GLU Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU Q 193 " --> pdb=" O GLU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 Processing helix chain 'Q' and resid 223 through 232 removed outlier: 3.882A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 248 removed outlier: 5.469A pdb=" N ASP Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE Q 244 " --> pdb=" O LYS Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 268 removed outlier: 3.738A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER Q 268 " --> pdb=" O LYS Q 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 267 removed outlier: 4.256A pdb=" N GLU U 257 " --> pdb=" O ILE U 253 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS U 262 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 369 removed outlier: 4.197A pdb=" N GLN U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 319 " --> pdb=" O LYS U 315 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 4.169A pdb=" N GLU U 346 " --> pdb=" O ASP U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 375 removed outlier: 4.061A pdb=" N GLU U 375 " --> pdb=" O VAL U 371 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 399 removed outlier: 4.506A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 415 Processing helix chain 'R' and resid 85 through 105 removed outlier: 4.236A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 114 removed outlier: 3.666A pdb=" N GLU R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.847A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 4.337A pdb=" N LYS R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 removed outlier: 4.024A pdb=" N ILE R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 472 removed outlier: 4.341A pdb=" N HIS T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 506 removed outlier: 4.158A pdb=" N MET T 482 " --> pdb=" O LYS T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.657A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.776A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.942A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.743A pdb=" N LEU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.630A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 37 removed outlier: 4.163A pdb=" N LEU S 36 " --> pdb=" O GLU S 32 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.818A pdb=" N GLU S 59 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN S 60 " --> pdb=" O ARG S 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.687A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'X' and resid 4 through 15 removed outlier: 3.512A pdb=" N VAL X 8 " --> pdb=" O ARG X 4 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS X 15 " --> pdb=" O LEU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 54 removed outlier: 3.564A pdb=" N VAL X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU X 33 " --> pdb=" O GLN X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 74 removed outlier: 3.691A pdb=" N VAL X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 68 - end of helix removed outlier: 3.563A pdb=" N LEU X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA2, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU L 240 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL L 307 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU L 238 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N LEU N 294 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLU N 272 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LYS N 296 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N LYS N 270 " --> pdb=" O LYS N 296 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N SER N 298 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N GLN N 268 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE N 266 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU N 264 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'M' and resid 128 through 130 removed outlier: 6.477A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 126 removed outlier: 4.687A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA N 161 " --> pdb=" O PHE N 86 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.773A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 128 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL O 143 " --> pdb=" O ILE O 150 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE O 150 " --> pdb=" O VAL O 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 217 through 224 removed outlier: 3.883A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE O 231 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.139A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR P 115 " --> pdb=" O MET P 142 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET P 142 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA P 134 " --> pdb=" O LEU P 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.620A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU P 217 " --> pdb=" O LYS P 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 241 " --> pdb=" O GLU P 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'T' and resid 550 through 552 Processing sheet with id=AB6, first strand: chain 'S' and resid 76 through 77 1569 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 10.66 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4252 1.31 - 1.43: 7236 1.43 - 1.56: 15661 1.56 - 1.68: 162 1.68 - 1.81: 216 Bond restraints: 27527 Sorted by residual: bond pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.24e-02 6.50e+03 2.03e+01 bond pdb=" C TRP L 72 " pdb=" O TRP L 72 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C GLN L 71 " pdb=" O GLN L 71 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" CA GLN L 71 " pdb=" C GLN L 71 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C1' DG J 15 " pdb=" N9 DG J 15 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 27522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 37008 1.91 - 3.82: 397 3.82 - 5.73: 56 5.73 - 7.63: 12 7.63 - 9.54: 1 Bond angle restraints: 37474 Sorted by residual: angle pdb=" O3' DA i 17 " pdb=" C3' DA i 17 " pdb=" C2' DA i 17 " ideal model delta sigma weight residual 111.50 101.96 9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" N GLU N 128 " pdb=" CA GLU N 128 " pdb=" C GLU N 128 " ideal model delta sigma weight residual 113.56 106.25 7.31 1.39e+00 5.18e-01 2.77e+01 angle pdb=" CA HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 116.21 122.22 -6.01 1.29e+00 6.01e-01 2.17e+01 angle pdb=" O HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 122.41 116.55 5.86 1.34e+00 5.57e-01 1.91e+01 angle pdb=" N LYS L 70 " pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 109.24 102.78 6.46 1.51e+00 4.39e-01 1.83e+01 ... (remaining 37469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14757 17.90 - 35.80: 1265 35.80 - 53.70: 486 53.70 - 71.60: 118 71.60 - 89.50: 28 Dihedral angle restraints: 16654 sinusoidal: 7403 harmonic: 9251 Sorted by residual: dihedral pdb=" CA GLN H 122 " pdb=" C GLN H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA CYS P 111 " pdb=" C CYS P 111 " pdb=" N HIS P 112 " pdb=" CA HIS P 112 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER H 124 " pdb=" C SER H 124 " pdb=" N VAL H 125 " pdb=" CA VAL H 125 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 16651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3942 0.064 - 0.129: 347 0.129 - 0.193: 9 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" C3' DA i 17 " pdb=" C4' DA i 17 " pdb=" O3' DA i 17 " pdb=" C2' DA i 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.98 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE K 82 " pdb=" CA ILE K 82 " pdb=" CG1 ILE K 82 " pdb=" CG2 ILE K 82 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' DT J 3 " pdb=" C4' DT J 3 " pdb=" O3' DT J 3 " pdb=" C2' DT J 3 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 4297 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 111 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C CYS P 111 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS P 111 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS P 112 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 16 " -0.025 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA i 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA i 16 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA i 16 " -0.011 2.00e-02 2.50e+03 pdb=" N6 DA i 16 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA i 16 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DA i 16 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA i 16 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT i 21 " -0.024 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" N1 DT i 21 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DT i 21 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT i 21 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DT i 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT i 21 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT i 21 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DT i 21 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT i 21 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT i 21 " 0.015 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 11199 2.95 - 3.60: 39754 3.60 - 4.25: 59170 4.25 - 4.90: 99120 Nonbonded interactions: 209265 Sorted by model distance: nonbonded pdb=" N3 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.653 3.200 nonbonded pdb=" C2' DA i 20 " pdb=" C7 DT i 21 " model vdw 1.767 3.860 nonbonded pdb=" N1 DG J 5 " pdb=" N1 DG i -3 " model vdw 1.772 3.200 nonbonded pdb=" C2 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.832 3.340 nonbonded pdb=" C2 DG J 5 " pdb=" C2 DG i -3 " model vdw 1.919 3.480 ... (remaining 209260 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.190 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 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:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 0.071 27527 Z= 0.165 Angle : 0.510 9.542 37474 Z= 0.302 Chirality : 0.037 0.322 4300 Planarity : 0.003 0.044 4432 Dihedral : 16.184 89.496 10582 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.82 % Allowed : 8.35 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.67 (0.14), residues: 3064 helix: 0.27 (0.11), residues: 1899 sheet: -0.32 (0.29), residues: 307 loop : -1.96 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 72 HIS 0.003 0.000 HIS P 112 PHE 0.013 0.001 PHE I 482 TYR 0.012 0.001 TYR O 239 ARG 0.003 0.000 ARG S 56 Details of bonding type rmsd hydrogen bonds : bond 0.12180 ( 1642) hydrogen bonds : angle 4.81748 ( 4789) covalent geometry : bond 0.00315 (27527) covalent geometry : angle 0.51031 (37474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 2.889 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: Q 93 MET cc_start: 0.8997 (ttp) cc_final: 0.8670 (tmt) REVERT: U 289 PHE cc_start: 0.8464 (m-10) cc_final: 0.8048 (m-80) REVERT: U 383 ASP cc_start: 0.7612 (p0) cc_final: 0.7198 (p0) REVERT: U 406 ASN cc_start: 0.8736 (m-40) cc_final: 0.8368 (m-40) REVERT: R 86 PHE cc_start: 0.4342 (m-80) cc_final: 0.4071 (m-10) REVERT: R 87 MET cc_start: 0.7825 (mmm) cc_final: 0.7463 (mmp) REVERT: T 478 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8747 (mmmm) REVERT: S 13 PHE cc_start: 0.8452 (t80) cc_final: 0.7881 (t80) REVERT: S 57 GLN cc_start: 0.7745 (tp40) cc_final: 0.7141 (tm-30) REVERT: X 5 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7589 (mmtt) REVERT: X 6 GLU cc_start: 0.6962 (tp30) cc_final: 0.6644 (tp30) REVERT: X 41 GLU cc_start: 0.8466 (tp30) cc_final: 0.7903 (tp30) REVERT: X 49 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8872 (tm-30) REVERT: X 69 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8702 (tm-30) outliers start: 23 outliers final: 10 residues processed: 350 average time/residue: 1.9028 time to fit residues: 748.1513 Evaluate side-chains 241 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 231 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain X residue 59 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 0.0010 chunk 247 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 182 GLN H 191 ASN H 203 GLN I 97 ASN I 193 GLN I 236 GLN I 349 GLN I 352 GLN I 374 HIS I 394 GLN I 429 GLN I 513 HIS I 726 GLN L 51 GLN L 201 GLN L 294 HIS M 156 HIS N 78 GLN N 80 GLN N 177 GLN N 185 HIS O 198 GLN O 267 GLN P 105 HIS P 112 HIS Q 111 ASN Q 177 GLN Q 181 ASN Q 202 GLN Q 204 ASN U 406 ASN R 130 HIS R 147 ASN T 456 HIS ** T 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 555 ASN X 29 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.085987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053208 restraints weight = 89125.444| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.03 r_work: 0.2883 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27527 Z= 0.130 Angle : 0.540 11.455 37474 Z= 0.286 Chirality : 0.038 0.214 4300 Planarity : 0.004 0.050 4432 Dihedral : 16.294 120.963 4233 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 1.99 % Allowed : 13.40 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.70 (0.15), residues: 3064 helix: 1.34 (0.12), residues: 1925 sheet: 0.05 (0.29), residues: 304 loop : -1.40 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 718 HIS 0.017 0.001 HIS P 112 PHE 0.026 0.001 PHE O 287 TYR 0.017 0.001 TYR P 196 ARG 0.014 0.001 ARG S 56 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1642) hydrogen bonds : angle 3.61871 ( 4789) covalent geometry : bond 0.00281 (27527) covalent geometry : angle 0.54020 (37474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 3.126 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: H 40 MET cc_start: 0.8815 (mmm) cc_final: 0.8389 (mmt) REVERT: O 25 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: P 206 MET cc_start: 0.6803 (ttp) cc_final: 0.6564 (ttt) REVERT: Q 93 MET cc_start: 0.9349 (ttp) cc_final: 0.8870 (tmt) REVERT: U 325 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: U 406 ASN cc_start: 0.8771 (m110) cc_final: 0.8449 (m-40) REVERT: R 86 PHE cc_start: 0.5080 (m-80) cc_final: 0.4731 (m-10) REVERT: R 87 MET cc_start: 0.8176 (mmm) cc_final: 0.7929 (mmp) REVERT: R 101 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7284 (mpt) REVERT: R 104 MET cc_start: 0.8447 (tpt) cc_final: 0.8146 (mmm) REVERT: T 476 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7048 (mt-10) REVERT: T 482 MET cc_start: 0.8271 (tpp) cc_final: 0.8030 (tpp) REVERT: T 508 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7556 (tmtt) REVERT: T 526 THR cc_start: 0.3706 (OUTLIER) cc_final: 0.3445 (p) REVERT: W 1 MET cc_start: 0.7224 (pmm) cc_final: 0.6751 (pmm) REVERT: S 57 GLN cc_start: 0.7059 (tp40) cc_final: 0.6399 (tm-30) REVERT: S 73 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8775 (mtpt) REVERT: X 5 LYS cc_start: 0.7416 (mmmm) cc_final: 0.6900 (mmtt) REVERT: X 41 GLU cc_start: 0.7929 (tp30) cc_final: 0.7332 (tp30) REVERT: X 48 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7699 (mtm110) REVERT: X 49 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8420 (tm-30) REVERT: X 69 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8427 (tp-100) outliers start: 56 outliers final: 17 residues processed: 304 average time/residue: 1.7945 time to fit residues: 616.9682 Evaluate side-chains 247 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 410 HIS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain U residue 395 ARG Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 274 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 0.0470 chunk 237 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 262 optimal weight: 0.0060 chunk 239 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS R 130 HIS T 545 GLN S 11 GLN S 24 HIS X 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.086041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053047 restraints weight = 89325.127| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.07 r_work: 0.2876 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27527 Z= 0.118 Angle : 0.536 9.998 37474 Z= 0.282 Chirality : 0.037 0.194 4300 Planarity : 0.003 0.051 4432 Dihedral : 16.142 79.286 4223 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 14.72 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.33 (0.15), residues: 3064 helix: 1.81 (0.12), residues: 1930 sheet: 0.25 (0.29), residues: 304 loop : -1.09 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.008 0.001 HIS P 112 PHE 0.027 0.001 PHE O 287 TYR 0.015 0.001 TYR I 72 ARG 0.006 0.000 ARG U 268 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 1642) hydrogen bonds : angle 3.46327 ( 4789) covalent geometry : bond 0.00251 (27527) covalent geometry : angle 0.53558 (37474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 4.790 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: H 40 MET cc_start: 0.8818 (mmm) cc_final: 0.8567 (mmt) REVERT: H 123 SER cc_start: 0.4686 (OUTLIER) cc_final: 0.4302 (m) REVERT: I 133 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6177 (mmm) REVERT: I 171 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7697 (mtt) REVERT: I 514 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5781 (mpp) REVERT: N 18 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: O 25 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: Q 93 MET cc_start: 0.9359 (ttp) cc_final: 0.8887 (tmt) REVERT: U 406 ASN cc_start: 0.8684 (m110) cc_final: 0.8328 (m-40) REVERT: R 86 PHE cc_start: 0.5175 (m-80) cc_final: 0.4826 (m-10) REVERT: R 87 MET cc_start: 0.8258 (mmm) cc_final: 0.7988 (mmp) REVERT: R 104 MET cc_start: 0.8516 (tpt) cc_final: 0.7544 (ptm) REVERT: T 476 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7240 (mt-10) REVERT: T 478 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8867 (mmmm) REVERT: T 481 GLU cc_start: 0.8419 (pm20) cc_final: 0.8195 (pm20) REVERT: T 526 THR cc_start: 0.3661 (OUTLIER) cc_final: 0.3386 (p) REVERT: W 1 MET cc_start: 0.7152 (pmm) cc_final: 0.6577 (pmm) REVERT: S 57 GLN cc_start: 0.7025 (tp40) cc_final: 0.6377 (tm-30) REVERT: S 73 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8794 (mtpt) REVERT: X 5 LYS cc_start: 0.7324 (mmmm) cc_final: 0.6018 (mmtt) REVERT: X 6 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6374 (tm-30) REVERT: X 29 GLN cc_start: 0.9223 (tp40) cc_final: 0.8686 (mp10) REVERT: X 33 GLU cc_start: 0.8119 (tp30) cc_final: 0.7575 (tp30) REVERT: X 41 GLU cc_start: 0.7897 (tp30) cc_final: 0.7468 (tm-30) REVERT: X 45 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7941 (mmt90) REVERT: X 49 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8443 (tm-30) REVERT: X 64 GLU cc_start: 0.8468 (mp0) cc_final: 0.8175 (mp0) REVERT: X 69 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8453 (tp-100) outliers start: 56 outliers final: 13 residues processed: 289 average time/residue: 2.4630 time to fit residues: 810.7819 Evaluate side-chains 245 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 6.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain U residue 407 ILE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain X residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 64 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN I 513 HIS N 177 GLN P 112 HIS R 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.084755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051452 restraints weight = 89270.306| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.08 r_work: 0.2828 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27527 Z= 0.137 Angle : 0.550 9.999 37474 Z= 0.289 Chirality : 0.038 0.186 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.122 79.549 4218 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.92 % Allowed : 15.82 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.66 (0.16), residues: 3064 helix: 2.05 (0.12), residues: 1935 sheet: 0.46 (0.30), residues: 296 loop : -0.96 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.004 0.001 HIS H 214 PHE 0.025 0.001 PHE O 287 TYR 0.015 0.001 TYR I 72 ARG 0.014 0.001 ARG X 48 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 1642) hydrogen bonds : angle 3.47065 ( 4789) covalent geometry : bond 0.00308 (27527) covalent geometry : angle 0.54958 (37474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 3.958 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: H 40 MET cc_start: 0.8885 (mmm) cc_final: 0.8632 (mmt) REVERT: H 123 SER cc_start: 0.5174 (OUTLIER) cc_final: 0.4858 (m) REVERT: I 128 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8894 (ptm160) REVERT: I 514 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.5839 (mpp) REVERT: L 113 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7673 (mm-30) REVERT: M 86 ARG cc_start: 0.9064 (mtm110) cc_final: 0.8798 (mtm-85) REVERT: N 18 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8669 (tpt) REVERT: O 25 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: Q 93 MET cc_start: 0.9378 (ttp) cc_final: 0.8873 (tmt) REVERT: Q 147 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8018 (mtp85) REVERT: U 309 MET cc_start: 0.8193 (ttp) cc_final: 0.7954 (ttp) REVERT: U 406 ASN cc_start: 0.8734 (m110) cc_final: 0.8385 (m-40) REVERT: R 86 PHE cc_start: 0.5201 (m-80) cc_final: 0.4845 (m-10) REVERT: R 87 MET cc_start: 0.8190 (mmm) cc_final: 0.7926 (mmp) REVERT: R 104 MET cc_start: 0.8586 (tpt) cc_final: 0.8205 (mmm) REVERT: T 476 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7336 (mt-10) REVERT: T 478 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8960 (mmmm) REVERT: W 1 MET cc_start: 0.7194 (pmm) cc_final: 0.6619 (pmm) REVERT: X 6 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6567 (tm-30) REVERT: X 20 LYS cc_start: 0.8383 (tmtm) cc_final: 0.8178 (tptp) REVERT: X 33 GLU cc_start: 0.8280 (tp30) cc_final: 0.7825 (tp30) REVERT: X 41 GLU cc_start: 0.7890 (tp30) cc_final: 0.7518 (tm-30) REVERT: X 45 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7972 (mmt90) REVERT: X 49 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8369 (tm-30) REVERT: X 64 GLU cc_start: 0.8521 (mp0) cc_final: 0.8178 (mp0) REVERT: X 69 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8457 (tp-100) outliers start: 54 outliers final: 17 residues processed: 282 average time/residue: 1.8299 time to fit residues: 587.1144 Evaluate side-chains 243 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 407 ILE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 315 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 HIS I 638 GLN P 112 HIS R 111 GLN R 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.083002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049536 restraints weight = 87966.415| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.04 r_work: 0.2775 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27527 Z= 0.177 Angle : 0.584 9.850 37474 Z= 0.309 Chirality : 0.040 0.179 4300 Planarity : 0.004 0.053 4432 Dihedral : 16.172 80.108 4218 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 16.71 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.70 (0.16), residues: 3064 helix: 2.06 (0.12), residues: 1941 sheet: 0.52 (0.30), residues: 296 loop : -0.93 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 718 HIS 0.008 0.001 HIS P 112 PHE 0.025 0.002 PHE Q 257 TYR 0.021 0.001 TYR S 15 ARG 0.004 0.000 ARG R 117 Details of bonding type rmsd hydrogen bonds : bond 0.05820 ( 1642) hydrogen bonds : angle 3.57367 ( 4789) covalent geometry : bond 0.00416 (27527) covalent geometry : angle 0.58365 (37474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 2.808 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: H 40 MET cc_start: 0.8932 (mmm) cc_final: 0.8657 (mmt) REVERT: H 60 MET cc_start: 0.9232 (tpp) cc_final: 0.8146 (mpp) REVERT: H 247 MET cc_start: 0.8597 (mtt) cc_final: 0.8318 (mtm) REVERT: I 128 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8916 (ptm160) REVERT: I 514 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.5710 (mpp) REVERT: L 113 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7764 (mm-30) REVERT: M 86 ARG cc_start: 0.9059 (mtm110) cc_final: 0.8800 (mtm180) REVERT: N 18 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8658 (mmm) REVERT: O 25 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8428 (tp30) REVERT: P 244 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7789 (tm-30) REVERT: Q 87 MET cc_start: 0.8859 (tpt) cc_final: 0.8509 (tpp) REVERT: Q 93 MET cc_start: 0.9385 (ttp) cc_final: 0.8786 (tmt) REVERT: Q 116 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7235 (ptm160) REVERT: Q 147 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8057 (mtp85) REVERT: Q 203 ILE cc_start: 0.7312 (mm) cc_final: 0.6685 (tp) REVERT: U 289 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: U 352 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8869 (tmm-80) REVERT: U 406 ASN cc_start: 0.8735 (m110) cc_final: 0.8382 (m-40) REVERT: R 86 PHE cc_start: 0.5222 (m-80) cc_final: 0.4855 (m-10) REVERT: R 87 MET cc_start: 0.8228 (mmm) cc_final: 0.7974 (mmp) REVERT: R 104 MET cc_start: 0.8507 (tpt) cc_final: 0.7503 (ptm) REVERT: T 476 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7414 (mt-10) REVERT: T 508 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7680 (tptp) REVERT: W 1 MET cc_start: 0.7265 (pmm) cc_final: 0.7007 (pmm) REVERT: X 6 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6491 (tm-30) REVERT: X 20 LYS cc_start: 0.8482 (tmtm) cc_final: 0.8266 (tptp) REVERT: X 33 GLU cc_start: 0.8396 (tp30) cc_final: 0.7901 (tp30) REVERT: X 41 GLU cc_start: 0.7976 (tp30) cc_final: 0.7747 (mm-30) REVERT: X 45 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8025 (mtt-85) REVERT: X 49 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8368 (tm-30) REVERT: X 64 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: X 69 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8422 (tp-100) outliers start: 58 outliers final: 18 residues processed: 281 average time/residue: 1.6884 time to fit residues: 538.3505 Evaluate side-chains 246 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 289 PHE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 203 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 HIS ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN M 144 GLN P 112 HIS Q 142 ASN R 130 HIS R 147 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.083976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050758 restraints weight = 88909.817| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.07 r_work: 0.2812 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27527 Z= 0.125 Angle : 0.566 11.899 37474 Z= 0.296 Chirality : 0.038 0.186 4300 Planarity : 0.003 0.051 4432 Dihedral : 16.074 80.927 4218 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.60 % Allowed : 18.02 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.90 (0.16), residues: 3064 helix: 2.20 (0.12), residues: 1942 sheet: 0.62 (0.30), residues: 297 loop : -0.79 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 718 HIS 0.008 0.001 HIS P 112 PHE 0.026 0.001 PHE O 287 TYR 0.021 0.001 TYR S 25 ARG 0.008 0.000 ARG K 26 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 1642) hydrogen bonds : angle 3.44976 ( 4789) covalent geometry : bond 0.00266 (27527) covalent geometry : angle 0.56645 (37474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 3.031 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: H 40 MET cc_start: 0.8939 (mmm) cc_final: 0.8580 (mmt) REVERT: H 127 MET cc_start: 0.8615 (mmm) cc_final: 0.8347 (mpp) REVERT: I 128 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8914 (ptm160) REVERT: I 268 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8133 (tt) REVERT: I 514 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.5710 (mpp) REVERT: L 113 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7719 (mm-30) REVERT: M 86 ARG cc_start: 0.9055 (mtm110) cc_final: 0.8749 (mtm-85) REVERT: N 18 MET cc_start: 0.8975 (mmm) cc_final: 0.8672 (tpt) REVERT: O 25 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8364 (tp30) REVERT: P 112 HIS cc_start: 0.8443 (t-90) cc_final: 0.8040 (t-170) REVERT: Q 87 MET cc_start: 0.8942 (tpt) cc_final: 0.8586 (tpp) REVERT: Q 93 MET cc_start: 0.9376 (ttp) cc_final: 0.8752 (tmt) REVERT: Q 147 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8053 (mtp85) REVERT: Q 203 ILE cc_start: 0.7384 (mm) cc_final: 0.6752 (tp) REVERT: U 309 MET cc_start: 0.8137 (ttp) cc_final: 0.7903 (ttt) REVERT: U 406 ASN cc_start: 0.8690 (m110) cc_final: 0.8367 (m-40) REVERT: R 86 PHE cc_start: 0.5261 (m-80) cc_final: 0.4894 (m-10) REVERT: R 87 MET cc_start: 0.8203 (mmm) cc_final: 0.7913 (mmp) REVERT: R 104 MET cc_start: 0.8472 (tpt) cc_final: 0.7514 (ptm) REVERT: R 134 ARG cc_start: 0.8762 (ttp-170) cc_final: 0.8468 (ptt90) REVERT: T 476 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7385 (mt-10) REVERT: T 508 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7607 (tptp) REVERT: W 1 MET cc_start: 0.7128 (pmm) cc_final: 0.6895 (pmm) REVERT: X 33 GLU cc_start: 0.8407 (tp30) cc_final: 0.7867 (tp30) REVERT: X 41 GLU cc_start: 0.7964 (tp30) cc_final: 0.7663 (mm-30) REVERT: X 45 ARG cc_start: 0.8248 (mmt90) cc_final: 0.8046 (mtt-85) REVERT: X 49 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8311 (tm-30) REVERT: X 64 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: X 69 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8407 (tp-100) outliers start: 45 outliers final: 19 residues processed: 273 average time/residue: 1.7415 time to fit residues: 537.0951 Evaluate side-chains 244 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 508 LYS Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 277 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 0.0370 chunk 285 optimal weight: 3.9990 chunk 157 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS T 545 GLN S 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.085133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052132 restraints weight = 89109.923| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.09 r_work: 0.2855 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27527 Z= 0.117 Angle : 0.563 10.319 37474 Z= 0.294 Chirality : 0.037 0.188 4300 Planarity : 0.003 0.050 4432 Dihedral : 15.906 80.995 4218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.53 % Allowed : 18.91 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.00 (0.16), residues: 3064 helix: 2.24 (0.12), residues: 1941 sheet: 0.66 (0.30), residues: 302 loop : -0.68 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 718 HIS 0.004 0.000 HIS U 265 PHE 0.028 0.001 PHE O 287 TYR 0.022 0.001 TYR I 72 ARG 0.016 0.000 ARG X 48 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 1642) hydrogen bonds : angle 3.34969 ( 4789) covalent geometry : bond 0.00242 (27527) covalent geometry : angle 0.56252 (37474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 2.882 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: H 40 MET cc_start: 0.8937 (mmm) cc_final: 0.8714 (mmt) REVERT: H 119 ILE cc_start: 0.9219 (mp) cc_final: 0.8732 (tp) REVERT: H 204 MET cc_start: 0.7688 (mmm) cc_final: 0.7406 (ppp) REVERT: I 128 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8897 (ptm160) REVERT: I 133 MET cc_start: 0.6970 (mmt) cc_final: 0.6761 (mmp) REVERT: I 514 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5746 (mpp) REVERT: L 113 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7612 (mm-30) REVERT: M 86 ARG cc_start: 0.9029 (mtm110) cc_final: 0.8747 (mtm-85) REVERT: N 18 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8564 (mmm) REVERT: O 25 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: Q 87 MET cc_start: 0.8970 (tpt) cc_final: 0.8638 (tpp) REVERT: Q 93 MET cc_start: 0.9380 (ttp) cc_final: 0.8820 (tmt) REVERT: Q 147 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8063 (mtp85) REVERT: Q 203 ILE cc_start: 0.7391 (mm) cc_final: 0.6738 (tp) REVERT: U 309 MET cc_start: 0.8093 (ttp) cc_final: 0.7806 (ttt) REVERT: U 406 ASN cc_start: 0.8725 (m110) cc_final: 0.8394 (m-40) REVERT: T 476 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7486 (mt-10) REVERT: T 508 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7835 (tptp) REVERT: S 38 LYS cc_start: 0.8775 (tppp) cc_final: 0.8329 (tttt) REVERT: S 45 GLN cc_start: 0.7941 (pm20) cc_final: 0.7722 (pm20) REVERT: X 6 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6774 (tm-30) REVERT: X 33 GLU cc_start: 0.8439 (tp30) cc_final: 0.7876 (tp30) REVERT: X 41 GLU cc_start: 0.7896 (tp30) cc_final: 0.7575 (mm-30) REVERT: X 49 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8267 (tm-30) REVERT: X 64 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: X 69 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8421 (tp-100) outliers start: 43 outliers final: 17 residues processed: 272 average time/residue: 1.7608 time to fit residues: 542.5685 Evaluate side-chains 246 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 508 LYS Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 306 optimal weight: 9.9990 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 106 GLN P 112 HIS R 130 HIS R 147 ASN S 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.084715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.051879 restraints weight = 87966.853| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.06 r_work: 0.2846 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27527 Z= 0.122 Angle : 0.588 11.884 37474 Z= 0.304 Chirality : 0.037 0.194 4300 Planarity : 0.003 0.050 4432 Dihedral : 15.861 80.723 4218 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.24 % Allowed : 19.77 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.08 (0.16), residues: 3064 helix: 2.29 (0.12), residues: 1939 sheet: 0.73 (0.31), residues: 302 loop : -0.60 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 718 HIS 0.007 0.001 HIS P 112 PHE 0.026 0.001 PHE O 287 TYR 0.022 0.001 TYR S 25 ARG 0.016 0.000 ARG X 48 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1642) hydrogen bonds : angle 3.33269 ( 4789) covalent geometry : bond 0.00265 (27527) covalent geometry : angle 0.58807 (37474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 3.119 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: H 119 ILE cc_start: 0.9242 (mp) cc_final: 0.8779 (tp) REVERT: I 128 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8886 (ptm160) REVERT: I 133 MET cc_start: 0.7123 (mmt) cc_final: 0.6920 (mmp) REVERT: I 514 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.5691 (mpp) REVERT: L 35 ARG cc_start: 0.8373 (tpm170) cc_final: 0.8167 (tpm170) REVERT: L 113 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7656 (mm-30) REVERT: M 86 ARG cc_start: 0.9029 (mtm110) cc_final: 0.8766 (mtm-85) REVERT: N 18 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: O 25 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: O 106 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8106 (mm-40) REVERT: P 112 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7969 (t-170) REVERT: Q 87 MET cc_start: 0.9064 (tpt) cc_final: 0.8674 (tpp) REVERT: Q 93 MET cc_start: 0.9381 (ttp) cc_final: 0.8804 (tmt) REVERT: Q 116 ARG cc_start: 0.7689 (mtm110) cc_final: 0.6963 (ptm160) REVERT: Q 147 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8079 (mtp85) REVERT: Q 203 ILE cc_start: 0.7487 (mm) cc_final: 0.6810 (tp) REVERT: U 309 MET cc_start: 0.8145 (ttp) cc_final: 0.7817 (ttp) REVERT: U 406 ASN cc_start: 0.8747 (m110) cc_final: 0.8414 (m-40) REVERT: R 104 MET cc_start: 0.8246 (tpt) cc_final: 0.7283 (ptm) REVERT: T 476 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7585 (mt-10) REVERT: T 508 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7848 (tptp) REVERT: W 1 MET cc_start: 0.6557 (pmm) cc_final: 0.6311 (pmm) REVERT: S 6 GLU cc_start: 0.8405 (tp30) cc_final: 0.7915 (pp20) REVERT: S 11 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8543 (pp30) REVERT: S 38 LYS cc_start: 0.8852 (tppp) cc_final: 0.8384 (tttt) REVERT: X 33 GLU cc_start: 0.8463 (tp30) cc_final: 0.7962 (tp30) REVERT: X 49 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8312 (tm-30) REVERT: X 59 ASP cc_start: 0.7588 (m-30) cc_final: 0.7325 (m-30) REVERT: X 64 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: X 69 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8450 (tp-100) outliers start: 35 outliers final: 18 residues processed: 259 average time/residue: 1.7933 time to fit residues: 524.4098 Evaluate side-chains 245 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 266 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 508 LYS Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 307 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS R 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049616 restraints weight = 87170.519| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.97 r_work: 0.2778 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27527 Z= 0.177 Angle : 0.644 12.380 37474 Z= 0.335 Chirality : 0.040 0.183 4300 Planarity : 0.004 0.073 4432 Dihedral : 15.952 80.529 4218 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 19.66 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.98 (0.16), residues: 3064 helix: 2.22 (0.12), residues: 1945 sheet: 0.66 (0.30), residues: 296 loop : -0.66 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 718 HIS 0.037 0.001 HIS P 112 PHE 0.024 0.001 PHE R 86 TYR 0.026 0.001 TYR I 72 ARG 0.012 0.001 ARG U 304 Details of bonding type rmsd hydrogen bonds : bond 0.05734 ( 1642) hydrogen bonds : angle 3.52826 ( 4789) covalent geometry : bond 0.00415 (27527) covalent geometry : angle 0.64356 (37474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 3.079 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: H 119 ILE cc_start: 0.9274 (mp) cc_final: 0.8837 (tp) REVERT: H 229 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: H 247 MET cc_start: 0.8480 (mtm) cc_final: 0.8276 (ptp) REVERT: I 128 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8901 (ptm160) REVERT: I 133 MET cc_start: 0.7150 (mmt) cc_final: 0.6868 (mmp) REVERT: I 514 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.5670 (mpp) REVERT: L 113 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7707 (mm-30) REVERT: M 86 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8799 (mtm180) REVERT: N 18 MET cc_start: 0.9008 (mmm) cc_final: 0.8660 (mmm) REVERT: O 25 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: Q 87 MET cc_start: 0.9043 (tpt) cc_final: 0.8674 (tpp) REVERT: Q 93 MET cc_start: 0.9368 (ttp) cc_final: 0.8782 (tmm) REVERT: Q 147 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8124 (mtp85) REVERT: U 309 MET cc_start: 0.8278 (ttp) cc_final: 0.7918 (ttp) REVERT: U 352 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8883 (tmm-80) REVERT: U 383 ASP cc_start: 0.7887 (p0) cc_final: 0.7620 (p0) REVERT: U 406 ASN cc_start: 0.8773 (m110) cc_final: 0.8437 (m-40) REVERT: R 104 MET cc_start: 0.8267 (tpt) cc_final: 0.7280 (ptm) REVERT: T 476 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7617 (mt-10) REVERT: W 1 MET cc_start: 0.6609 (pmm) cc_final: 0.6205 (pmm) REVERT: S 6 GLU cc_start: 0.8323 (tp30) cc_final: 0.7701 (pp20) REVERT: S 11 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8500 (tm-30) REVERT: S 12 ARG cc_start: 0.8888 (ptm160) cc_final: 0.8474 (ptm160) REVERT: S 38 LYS cc_start: 0.8865 (tppp) cc_final: 0.8406 (tttt) REVERT: X 20 LYS cc_start: 0.8436 (tptp) cc_final: 0.8183 (tptp) REVERT: X 33 GLU cc_start: 0.8505 (tp30) cc_final: 0.7972 (tp30) REVERT: X 41 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7592 (tm-30) REVERT: X 45 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7938 (mmt90) REVERT: X 49 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8416 (tm-30) REVERT: X 59 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: X 64 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: X 69 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8479 (tp-100) outliers start: 40 outliers final: 17 residues processed: 259 average time/residue: 1.8108 time to fit residues: 534.2330 Evaluate side-chains 240 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 290 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 310 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 112 HIS R 130 HIS T 545 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050154 restraints weight = 87315.803| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.00 r_work: 0.2796 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27527 Z= 0.147 Angle : 0.655 13.470 37474 Z= 0.338 Chirality : 0.039 0.213 4300 Planarity : 0.004 0.065 4432 Dihedral : 15.937 81.087 4217 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.21 % Allowed : 20.09 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.04 (0.16), residues: 3064 helix: 2.26 (0.12), residues: 1943 sheet: 0.66 (0.30), residues: 301 loop : -0.63 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.004 0.001 HIS I 91 PHE 0.026 0.001 PHE Q 257 TYR 0.030 0.001 TYR S 15 ARG 0.017 0.001 ARG X 48 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 1642) hydrogen bonds : angle 3.49744 ( 4789) covalent geometry : bond 0.00335 (27527) covalent geometry : angle 0.65505 (37474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 3.240 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: H 119 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8879 (tp) REVERT: H 184 ILE cc_start: 0.8587 (tp) cc_final: 0.8352 (mp) REVERT: H 229 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: I 128 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (ptm160) REVERT: I 133 MET cc_start: 0.7120 (mmt) cc_final: 0.6850 (mmp) REVERT: I 514 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.5683 (mpp) REVERT: L 35 ARG cc_start: 0.8362 (tpm170) cc_final: 0.7867 (tpm170) REVERT: L 113 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7688 (mm-30) REVERT: M 86 ARG cc_start: 0.9048 (mtm110) cc_final: 0.8746 (mtm180) REVERT: N 18 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8626 (mmm) REVERT: O 25 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: Q 93 MET cc_start: 0.9371 (ttp) cc_final: 0.8729 (tmt) REVERT: Q 147 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8130 (mtp85) REVERT: U 309 MET cc_start: 0.8277 (ttp) cc_final: 0.7898 (ttp) REVERT: U 406 ASN cc_start: 0.8738 (m110) cc_final: 0.8403 (m-40) REVERT: R 87 MET cc_start: 0.7917 (mpm) cc_final: 0.7618 (mmp) REVERT: R 104 MET cc_start: 0.8258 (tpt) cc_final: 0.7304 (ptt) REVERT: T 476 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7686 (mt-10) REVERT: W 1 MET cc_start: 0.6741 (pmm) cc_final: 0.6465 (pmm) REVERT: S 6 GLU cc_start: 0.8246 (tp30) cc_final: 0.7743 (pp20) REVERT: S 11 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8610 (pp30) REVERT: X 33 GLU cc_start: 0.8542 (tp30) cc_final: 0.8015 (tp30) REVERT: X 48 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7769 (mtm110) REVERT: X 49 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8403 (tm-30) REVERT: X 59 ASP cc_start: 0.7775 (m-30) cc_final: 0.7563 (m-30) REVERT: X 64 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: X 69 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8401 (tp-100) outliers start: 34 outliers final: 18 residues processed: 249 average time/residue: 1.8800 time to fit residues: 531.5214 Evaluate side-chains 237 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 246 MET Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 162 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 171 optimal weight: 0.0040 chunk 197 optimal weight: 0.1980 chunk 249 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 0.0060 chunk 8 optimal weight: 0.7980 overall best weight: 0.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 112 HIS Q 136 ASN R 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.084286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051548 restraints weight = 87883.706| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.98 r_work: 0.2840 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27527 Z= 0.127 Angle : 0.638 11.407 37474 Z= 0.329 Chirality : 0.038 0.215 4300 Planarity : 0.004 0.064 4432 Dihedral : 15.835 81.512 4217 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.10 % Allowed : 20.37 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.09 (0.16), residues: 3064 helix: 2.30 (0.12), residues: 1938 sheet: 0.72 (0.30), residues: 302 loop : -0.60 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 718 HIS 0.007 0.001 HIS P 112 PHE 0.026 0.001 PHE O 287 TYR 0.026 0.001 TYR S 15 ARG 0.016 0.000 ARG X 48 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1642) hydrogen bonds : angle 3.42084 ( 4789) covalent geometry : bond 0.00273 (27527) covalent geometry : angle 0.63796 (37474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26436.13 seconds wall clock time: 456 minutes 4.63 seconds (27364.63 seconds total)