Starting phenix.real_space_refine on Sat Feb 24 08:00:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsr_35004/02_2024/8hsr_35004_updated.pdb" } resolution = 4.0 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= -0.012 sd= 0.925 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 107 5.49 5 Mg 7 5.21 5 S 108 5.16 5 Be 6 3.05 5 C 26538 2.51 5 N 7594 2.21 5 O 8197 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42577 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "C" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2882 Classifications: {'peptide': 367} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 347} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8829 Classifications: {'peptide': 1119} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1046} Chain: "J" Number of atoms: 10280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1303, 10280 Classifications: {'peptide': 1303} Link IDs: {'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "T" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 786 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 474 Classifications: {'RNA': 29} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 20} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 5, ' C%rna3p_pyr:plan': 5, ' A%rna3p_pur:plan': 6, ' A%rna3p_pur:plan2': 6, ' U%rna3p_pyr:plan': 3} Unresolved non-hydrogen planarities: 146 Chain: "N" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 2, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 30011 SG CYS J 58 88.040 122.955 93.958 1.00375.92 S ATOM 30022 SG CYS J 60 86.625 126.287 95.266 1.00419.37 S ATOM 30133 SG CYS J 73 86.654 125.732 91.839 1.00414.55 S ATOM 30159 SG CYS J 76 90.307 125.689 93.717 1.00409.45 S ATOM 36892 SG CYS J1112 134.528 88.458 62.611 1.00111.30 S ATOM 37536 SG CYS J1194 133.604 88.470 66.256 1.00 96.16 S ATOM 37592 SG CYS J1201 132.151 85.849 64.020 1.00101.97 S ATOM 37616 SG CYS J1204 135.611 85.441 64.747 1.00 97.92 S Time building chain proxies: 21.32, per 1000 atoms: 0.50 Number of scatterers: 42577 At special positions: 0 Unit cell: (201.4, 210.94, 168.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 108 16.00 P 107 15.00 Mg 7 11.99 F 18 9.00 O 8197 8.00 N 7594 7.00 C 26538 6.00 Be 6 4.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM42407 O5' ADP A1000 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.32 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1601 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 58 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 60 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 73 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 76 " pdb=" ZN J1602 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1201 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1112 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1204 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1194 " Number of angles added : 12 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 49 sheets defined 36.3% alpha, 11.7% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 17.86 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.836A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'B' and resid 243 through 263 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.398A pdb=" N LEU B 301 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 302 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE B 303 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 243 through 262 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 300 through 309 Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.697A pdb=" N THR C 345 " --> pdb=" O GLU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 No H-bonds generated for 'chain 'C' and resid 375 through 378' Processing helix chain 'C' and resid 381 through 396 Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.744A pdb=" N ALA C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 219 through 228 Processing helix chain 'D' and resid 243 through 263 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 300 through 309 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 375 through 378 No H-bonds generated for 'chain 'D' and resid 375 through 378' Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'E' and resid 243 through 262 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 300 through 309 Proline residue: E 304 - end of helix Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 399 through 412 Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 219 through 229 Processing helix chain 'F' and resid 243 through 262 Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 300 through 309 Proline residue: F 304 - end of helix Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 381 through 396 removed outlier: 5.295A pdb=" N ASP F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'G' and resid 33 through 46 Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.913A pdb=" N GLU G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 153 through 156 No H-bonds generated for 'chain 'G' and resid 153 through 156' Processing helix chain 'G' and resid 207 through 225 removed outlier: 3.812A pdb=" N TYR G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE G 225 " --> pdb=" O HIS G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 47 Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 75 through 83 Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 153 through 156 No H-bonds generated for 'chain 'H' and resid 153 through 156' Processing helix chain 'H' and resid 207 through 225 removed outlier: 3.739A pdb=" N TYR H 224 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE H 225 " --> pdb=" O HIS H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 193 through 199 Processing helix chain 'I' and resid 204 through 210 Processing helix chain 'I' and resid 216 through 222 removed outlier: 3.742A pdb=" N GLN I 219 " --> pdb=" O GLU I 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET I 222 " --> pdb=" O GLN I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 241 Processing helix chain 'I' and resid 274 through 278 Processing helix chain 'I' and resid 303 through 315 Processing helix chain 'I' and resid 328 through 330 No H-bonds generated for 'chain 'I' and resid 328 through 330' Processing helix chain 'I' and resid 336 through 361 Processing helix chain 'I' and resid 376 through 388 Processing helix chain 'I' and resid 400 through 407 Processing helix chain 'I' and resid 488 through 493 removed outlier: 4.232A pdb=" N ARG I 493 " --> pdb=" O THR I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 528 No H-bonds generated for 'chain 'I' and resid 526 through 528' Processing helix chain 'I' and resid 536 through 539 Processing helix chain 'I' and resid 542 through 546 removed outlier: 3.638A pdb=" N LEU I 546 " --> pdb=" O VAL I 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 542 through 546' Processing helix chain 'I' and resid 550 through 552 No H-bonds generated for 'chain 'I' and resid 550 through 552' Processing helix chain 'I' and resid 555 through 566 removed outlier: 3.717A pdb=" N THR I 566 " --> pdb=" O SER I 562 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 590 Processing helix chain 'I' and resid 693 through 696 No H-bonds generated for 'chain 'I' and resid 693 through 696' Processing helix chain 'I' and resid 733 through 736 removed outlier: 3.583A pdb=" N ASP I 736 " --> pdb=" O ALA I 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 733 through 736' Processing helix chain 'I' and resid 769 through 779 Processing helix chain 'I' and resid 855 through 857 No H-bonds generated for 'chain 'I' and resid 855 through 857' Processing helix chain 'I' and resid 873 through 878 Proline residue: I 877 - end of helix Processing helix chain 'I' and resid 883 through 897 removed outlier: 3.721A pdb=" N PHE I 896 " --> pdb=" O LEU I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 911 through 932 removed outlier: 3.762A pdb=" N GLU I 932 " --> pdb=" O LYS I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 938 through 949 Processing helix chain 'I' and resid 959 through 968 Processing helix chain 'I' and resid 1035 through 1042 Processing helix chain 'I' and resid 1047 through 1053 Processing helix chain 'I' and resid 1060 through 1071 Processing helix chain 'I' and resid 1083 through 1094 Processing helix chain 'J' and resid 15 through 21 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 83 through 88 Processing helix chain 'J' and resid 102 through 106 Processing helix chain 'J' and resid 111 through 115 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.771A pdb=" N TYR J 163 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 426 No H-bonds generated for 'chain 'J' and resid 424 through 426' Processing helix chain 'J' and resid 457 through 467 Processing helix chain 'J' and resid 470 through 482 Processing helix chain 'J' and resid 486 through 504 removed outlier: 3.883A pdb=" N LYS J 491 " --> pdb=" O ALA J 487 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 512 Processing helix chain 'J' and resid 522 through 525 Processing helix chain 'J' and resid 539 through 560 Processing helix chain 'J' and resid 564 through 582 Processing helix chain 'J' and resid 603 through 607 Processing helix chain 'J' and resid 614 through 617 No H-bonds generated for 'chain 'J' and resid 614 through 617' Processing helix chain 'J' and resid 646 through 652 Processing helix chain 'J' and resid 654 through 663 Processing helix chain 'J' and resid 670 through 677 Processing helix chain 'J' and resid 680 through 682 No H-bonds generated for 'chain 'J' and resid 680 through 682' Processing helix chain 'J' and resid 685 through 694 Processing helix chain 'J' and resid 710 through 712 No H-bonds generated for 'chain 'J' and resid 710 through 712' Processing helix chain 'J' and resid 730 through 733 Processing helix chain 'J' and resid 753 through 762 Processing helix chain 'J' and resid 765 through 767 No H-bonds generated for 'chain 'J' and resid 765 through 767' Processing helix chain 'J' and resid 783 through 792 Processing helix chain 'J' and resid 812 through 821 Processing helix chain 'J' and resid 836 through 840 Processing helix chain 'J' and resid 846 through 854 Processing helix chain 'J' and resid 877 through 889 Processing helix chain 'J' and resid 894 through 898 Processing helix chain 'J' and resid 908 through 921 Processing helix chain 'J' and resid 925 through 945 Processing helix chain 'J' and resid 951 through 953 No H-bonds generated for 'chain 'J' and resid 951 through 953' Processing helix chain 'J' and resid 959 through 979 Processing helix chain 'J' and resid 985 through 1014 removed outlier: 3.701A pdb=" N GLU J1001 " --> pdb=" O THR J 997 " (cutoff:3.500A) Processing helix chain 'J' and resid 1019 through 1025 Processing helix chain 'J' and resid 1032 through 1039 Processing helix chain 'J' and resid 1067 through 1101 removed outlier: 3.838A pdb=" N HIS J1075 " --> pdb=" O PHE J1071 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY J1076 " --> pdb=" O ILE J1072 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA J1089 " --> pdb=" O ALA J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1144 Processing helix chain 'J' and resid 1168 through 1180 Processing helix chain 'J' and resid 1191 through 1193 No H-bonds generated for 'chain 'J' and resid 1191 through 1193' Processing helix chain 'J' and resid 1202 through 1205 No H-bonds generated for 'chain 'J' and resid 1202 through 1205' Processing helix chain 'J' and resid 1221 through 1235 Proline residue: J1232 - end of helix removed outlier: 4.530A pdb=" N GLN J1235 " --> pdb=" O GLU J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1256 through 1263 Processing helix chain 'J' and resid 1332 through 1338 Processing helix chain 'J' and resid 1341 through 1358 removed outlier: 3.722A pdb=" N VAL J1355 " --> pdb=" O GLU J1351 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR J1356 " --> pdb=" O ILE J1352 " (cutoff:3.500A) Processing helix chain 'J' and resid 1365 through 1376 Processing helix chain 'J' and resid 1395 through 1406 Processing helix chain 'J' and resid 1424 through 1429 Processing helix chain 'J' and resid 1434 through 1440 Processing helix chain 'J' and resid 1443 through 1452 Processing helix chain 'J' and resid 1462 through 1468 Processing helix chain 'J' and resid 1475 through 1477 No H-bonds generated for 'chain 'J' and resid 1475 through 1477' Processing helix chain 'J' and resid 1479 through 1482 No H-bonds generated for 'chain 'J' and resid 1479 through 1482' Processing helix chain 'J' and resid 1489 through 1502 Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 16 through 33 Processing helix chain 'K' and resid 53 through 55 No H-bonds generated for 'chain 'K' and resid 53 through 55' Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 82 through 91 removed outlier: 4.552A pdb=" N GLU K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 66 through 68 Processing sheet with id= B, first strand: chain 'A' and resid 348 through 351 removed outlier: 3.843A pdb=" N MET A 348 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY A 180 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 322 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE A 182 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 324 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA A 184 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA A 326 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 325 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS A 209 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 270 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A 211 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU A 233 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU A 214 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 235 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.690A pdb=" N GLN A 109 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 125 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 74 through 77 removed outlier: 6.510A pdb=" N GLN B 109 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL B 125 " --> pdb=" O GLN B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 Processing sheet with id= F, first strand: chain 'B' and resid 233 through 237 removed outlier: 3.575A pdb=" N GLU B 233 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER B 319 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE B 269 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 321 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 271 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 323 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 61 through 65 removed outlier: 6.103A pdb=" N GLN C 109 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL C 125 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 348 through 352 removed outlier: 8.198A pdb=" N GLY C 180 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 322 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE C 182 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA C 324 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA C 184 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA C 326 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 209 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU C 270 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE C 211 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU C 233 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU C 214 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE C 235 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ASP C 216 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER C 237 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 105 through 109 removed outlier: 3.762A pdb=" N TYR D 65 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 182 through 184 Processing sheet with id= K, first strand: chain 'D' and resid 233 through 237 removed outlier: 3.770A pdb=" N GLU D 233 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER D 319 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE D 269 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 321 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU D 271 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 323 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 62 through 64 Processing sheet with id= M, first strand: chain 'E' and resid 325 through 327 removed outlier: 5.592A pdb=" N ILE E 182 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU E 350 " --> pdb=" O VAL E 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 233 through 235 removed outlier: 4.070A pdb=" N GLU E 233 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER E 319 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE E 269 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR E 321 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU E 271 " --> pdb=" O THR E 321 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 323 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 62 through 65 removed outlier: 3.687A pdb=" N VAL F 62 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 108 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 179 through 184 removed outlier: 7.606A pdb=" N GLY F 180 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE F 322 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE F 182 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA F 324 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA F 184 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA F 326 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS F 209 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LEU F 270 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE F 211 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 233 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 10 through 16 removed outlier: 3.672A pdb=" N TYR G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 87 through 89 Processing sheet with id= S, first strand: chain 'G' and resid 96 through 104 removed outlier: 6.014A pdb=" N ASP G 145 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL G 53 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY G 147 " --> pdb=" O THR G 51 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR G 51 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 107 through 110 Processing sheet with id= U, first strand: chain 'H' and resid 10 through 16 removed outlier: 3.511A pdb=" N TYR H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= W, first strand: chain 'H' and resid 96 through 103 removed outlier: 6.640A pdb=" N ASP H 145 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL H 53 " --> pdb=" O ASP H 145 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY H 147 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR H 51 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 108 through 110 Processing sheet with id= Y, first strand: chain 'I' and resid 2 through 5 Processing sheet with id= Z, first strand: chain 'I' and resid 54 through 56 removed outlier: 6.631A pdb=" N ARG I 97 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR I 71 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR I 95 " --> pdb=" O TYR I 71 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 91 through 93 Processing sheet with id= AB, first strand: chain 'I' and resid 392 through 394 removed outlier: 3.757A pdb=" N ASN I 130 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG I 134 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE I 128 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 139 through 142 Processing sheet with id= AD, first strand: chain 'I' and resid 145 through 150 removed outlier: 6.367A pdb=" N TYR I 158 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 176 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 409 through 411 Processing sheet with id= AF, first strand: chain 'I' and resid 483 through 486 Processing sheet with id= AG, first strand: chain 'I' and resid 512 through 516 Processing sheet with id= AH, first strand: chain 'I' and resid 620 through 624 removed outlier: 5.832A pdb=" N ARG I 614 " --> pdb=" O VAL I 603 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL I 603 " --> pdb=" O ARG I 614 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 988 through 994 removed outlier: 4.544A pdb=" N VAL I 988 " --> pdb=" O ILE I 676 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL I 869 " --> pdb=" O ALA I 675 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 759 through 761 Processing sheet with id= AK, first strand: chain 'I' and resid 687 through 691 removed outlier: 6.082A pdb=" N VAL I 848 " --> pdb=" O ILE I 688 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE I 690 " --> pdb=" O VAL I 848 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA I 850 " --> pdb=" O ILE I 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'I' and resid 701 through 713 removed outlier: 3.710A pdb=" N ARG I 802 " --> pdb=" O TYR I 826 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA I 828 " --> pdb=" O VAL I 800 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL I 800 " --> pdb=" O ALA I 828 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 91 through 94 Processing sheet with id= AN, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.748A pdb=" N GLU J 183 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 399 through 402 Processing sheet with id= AP, first strand: chain 'J' and resid 527 through 529 Processing sheet with id= AQ, first strand: chain 'J' and resid 626 through 630 Processing sheet with id= AR, first strand: chain 'J' and resid 631 through 633 removed outlier: 5.714A pdb=" N ILE J 726 " --> pdb=" O VAL J 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'J' and resid 641 through 645 removed outlier: 5.830A pdb=" N GLN J 717 " --> pdb=" O CYS J 642 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU J 644 " --> pdb=" O GLN J 717 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL J 719 " --> pdb=" O LEU J 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'J' and resid 863 through 867 Processing sheet with id= AU, first strand: chain 'J' and resid 1118 through 1121 Processing sheet with id= AV, first strand: chain 'J' and resid 1280 through 1284 Processing sheet with id= AW, first strand: chain 'J' and resid 1392 through 1394 removed outlier: 4.390A pdb=" N TYR J1378 " --> pdb=" O LEU J1420 " (cutoff:3.500A) 1360 hydrogen bonds defined for protein. 3933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 17.40 Time building geometry restraints manager: 20.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9225 1.33 - 1.45: 9069 1.45 - 1.57: 24763 1.57 - 1.69: 204 1.69 - 1.82: 203 Bond restraints: 43464 Sorted by residual: bond pdb=" BE BEF A1002 " pdb=" F2 BEF A1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" BE BEF D1002 " pdb=" F2 BEF D1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" BE BEF E1002 " pdb=" F2 BEF E1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF F1002 " pdb=" F2 BEF F1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF C1004 " pdb=" F2 BEF C1004 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 43459 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.26: 1065 104.26 - 112.32: 22629 112.32 - 120.37: 18524 120.37 - 128.43: 16687 128.43 - 136.49: 268 Bond angle restraints: 59173 Sorted by residual: angle pdb=" N GLN F 97 " pdb=" CA GLN F 97 " pdb=" CB GLN F 97 " ideal model delta sigma weight residual 110.07 117.42 -7.35 1.45e+00 4.76e-01 2.57e+01 angle pdb=" N GLU E 78 " pdb=" CA GLU E 78 " pdb=" C GLU E 78 " ideal model delta sigma weight residual 108.07 114.79 -6.72 1.38e+00 5.25e-01 2.37e+01 angle pdb=" N VAL I 254 " pdb=" CA VAL I 254 " pdb=" C VAL I 254 " ideal model delta sigma weight residual 113.42 107.87 5.55 1.17e+00 7.31e-01 2.25e+01 angle pdb=" C3' DC T 21 " pdb=" O3' DC T 21 " pdb=" P DA T 22 " ideal model delta sigma weight residual 120.20 127.21 -7.01 1.50e+00 4.44e-01 2.18e+01 angle pdb=" F2 BEF B 502 " pdb=" BE BEF B 502 " pdb=" F3 BEF B 502 " ideal model delta sigma weight residual 119.96 106.27 13.69 3.00e+00 1.11e-01 2.08e+01 ... (remaining 59168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 26030 35.65 - 71.30: 588 71.30 - 106.96: 43 106.96 - 142.61: 2 142.61 - 178.26: 5 Dihedral angle restraints: 26668 sinusoidal: 11892 harmonic: 14776 Sorted by residual: dihedral pdb=" C4' U R 13 " pdb=" C3' U R 13 " pdb=" C2' U R 13 " pdb=" C1' U R 13 " ideal model delta sinusoidal sigma weight residual 36.00 -36.29 72.29 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' U R 13 " pdb=" C4' U R 13 " pdb=" C3' U R 13 " pdb=" O3' U R 13 " ideal model delta sinusoidal sigma weight residual 82.00 148.37 -66.37 1 8.00e+00 1.56e-02 8.99e+01 dihedral pdb=" O4' U R 13 " pdb=" C2' U R 13 " pdb=" C1' U R 13 " pdb=" C3' U R 13 " ideal model delta sinusoidal sigma weight residual 25.00 -36.01 61.01 1 8.00e+00 1.56e-02 7.73e+01 ... (remaining 26665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5599 0.061 - 0.123: 1066 0.123 - 0.184: 86 0.184 - 0.246: 5 0.246 - 0.307: 4 Chirality restraints: 6760 Sorted by residual: chirality pdb=" CG LEU J 619 " pdb=" CB LEU J 619 " pdb=" CD1 LEU J 619 " pdb=" CD2 LEU J 619 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE I 163 " pdb=" CA ILE I 163 " pdb=" CG1 ILE I 163 " pdb=" CG2 ILE I 163 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P DG T 32 " pdb=" OP1 DG T 32 " pdb=" OP2 DG T 32 " pdb=" O5' DG T 32 " both_signs ideal model delta sigma weight residual True 2.35 -2.62 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 6757 not shown) Planarity restraints: 7415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 286 " 0.083 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO B 287 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 286 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO C 287 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 287 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 287 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 57 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO K 58 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO K 58 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 58 " -0.038 5.00e-02 4.00e+02 ... (remaining 7412 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 35 1.97 - 2.71: 2174 2.71 - 3.44: 66801 3.44 - 4.17: 106797 4.17 - 4.90: 182545 Nonbonded interactions: 358352 Sorted by model distance: nonbonded pdb=" OE2 GLU B 217 " pdb=" F1 BEF B 502 " model vdw 1.243 2.390 nonbonded pdb=" OE2 GLU B 217 " pdb=" BE BEF B 502 " model vdw 1.301 2.420 nonbonded pdb=" O2B ADP A1000 " pdb=" F2 BEF A1002 " model vdw 1.328 2.390 nonbonded pdb=" C2 DG T 1 " pdb=" O2 DC N 41 " model vdw 1.354 3.260 nonbonded pdb=" N1 DG T 1 " pdb=" O2 DC N 41 " model vdw 1.380 2.520 ... (remaining 358347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 420 or resid 1000)) selection = (chain 'B' and (resid 60 through 420 or resid 501)) selection = (chain 'C' and (resid 60 through 420 or resid 1002)) selection = (chain 'D' and (resid 60 through 420 or resid 1000)) selection = (chain 'E' and (resid 60 through 420 or resid 1000)) selection = (chain 'F' and (resid 60 through 420 or resid 1000)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.290 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 124.890 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 43464 Z= 0.318 Angle : 0.802 13.809 59173 Z= 0.414 Chirality : 0.046 0.307 6760 Planarity : 0.006 0.128 7415 Dihedral : 15.148 178.259 17142 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.14 % Rotamer: Outliers : 0.02 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.12), residues: 5117 helix: 0.24 (0.12), residues: 1835 sheet: -0.59 (0.19), residues: 710 loop : -0.92 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 388 HIS 0.010 0.002 HIS J1103 PHE 0.037 0.002 PHE B 252 TYR 0.033 0.002 TYR B 98 ARG 0.014 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 5.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 140 MET cc_start: 0.7886 (ppp) cc_final: 0.7457 (ppp) REVERT: J 456 MET cc_start: 0.4599 (ttt) cc_final: 0.4228 (ttp) REVERT: J 661 MET cc_start: 0.9105 (ppp) cc_final: 0.8704 (ppp) REVERT: J 1219 GLU cc_start: 0.8445 (pp20) cc_final: 0.8188 (pp20) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.5196 time to fit residues: 281.4438 Evaluate side-chains 222 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 436 optimal weight: 4.9990 chunk 391 optimal weight: 40.0000 chunk 217 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 chunk 264 optimal weight: 0.0270 chunk 209 optimal weight: 10.0000 chunk 405 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 469 optimal weight: 10.0000 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 97 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 HIS ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 593 ASN ** J 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43464 Z= 0.233 Angle : 0.684 12.085 59173 Z= 0.340 Chirality : 0.044 0.220 6760 Planarity : 0.005 0.123 7415 Dihedral : 14.443 174.700 6870 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 0.71 % Allowed : 7.40 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 5117 helix: 0.38 (0.12), residues: 1876 sheet: -0.64 (0.19), residues: 746 loop : -0.90 (0.13), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 21 HIS 0.006 0.001 HIS E 81 PHE 0.028 0.002 PHE F 362 TYR 0.027 0.001 TYR J1207 ARG 0.009 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.2779 (tp) cc_final: 0.2478 (tt) REVERT: B 334 MET cc_start: 0.1947 (ttt) cc_final: 0.1716 (mtt) REVERT: B 397 MET cc_start: 0.4416 (pmm) cc_final: 0.4056 (pmm) REVERT: I 229 MET cc_start: 0.6880 (mpp) cc_final: 0.6577 (mmm) REVERT: I 275 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: I 560 MET cc_start: 0.8508 (ptm) cc_final: 0.8232 (ptp) REVERT: I 880 MET cc_start: 0.8045 (mpp) cc_final: 0.7819 (mpp) REVERT: J 661 MET cc_start: 0.9154 (ppp) cc_final: 0.8775 (ppp) REVERT: J 1219 GLU cc_start: 0.8526 (pp20) cc_final: 0.8243 (pp20) REVERT: K 52 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7839 (mm-30) outliers start: 31 outliers final: 19 residues processed: 272 average time/residue: 0.5047 time to fit residues: 236.7961 Evaluate side-chains 237 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 260 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 390 optimal weight: 40.0000 chunk 319 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 470 optimal weight: 7.9990 chunk 508 optimal weight: 6.9990 chunk 418 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 377 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 97 GLN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1334 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 43464 Z= 0.376 Angle : 0.736 11.784 59173 Z= 0.369 Chirality : 0.044 0.182 6760 Planarity : 0.006 0.121 7415 Dihedral : 14.399 175.804 6870 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 1.61 % Allowed : 11.65 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.77 (0.12), residues: 5117 helix: 0.28 (0.12), residues: 1885 sheet: -0.71 (0.19), residues: 734 loop : -1.00 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 21 HIS 0.011 0.002 HIS A 254 PHE 0.027 0.002 PHE A 307 TYR 0.029 0.002 TYR J1207 ARG 0.010 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 227 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 MET cc_start: 0.5726 (mmm) cc_final: 0.5211 (mmm) REVERT: H 140 MET cc_start: 0.7981 (ppp) cc_final: 0.7500 (ppp) REVERT: I 229 MET cc_start: 0.6799 (mpp) cc_final: 0.6464 (mpp) REVERT: I 340 MET cc_start: 0.8763 (tmm) cc_final: 0.8289 (tmm) REVERT: I 880 MET cc_start: 0.8178 (mpp) cc_final: 0.7864 (mpp) REVERT: J 456 MET cc_start: 0.3703 (ttp) cc_final: 0.2835 (ttp) REVERT: J 481 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8623 (tpp) REVERT: J 661 MET cc_start: 0.9012 (ppp) cc_final: 0.8694 (ppp) REVERT: J 1219 GLU cc_start: 0.8622 (pp20) cc_final: 0.8313 (pp20) REVERT: K 52 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7759 (mm-30) outliers start: 70 outliers final: 47 residues processed: 276 average time/residue: 0.4931 time to fit residues: 237.5803 Evaluate side-chains 256 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 813 VAL Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 1098 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 464 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 472 optimal weight: 2.9990 chunk 499 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 447 optimal weight: 4.9990 chunk 134 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 43464 Z= 0.264 Angle : 0.669 12.170 59173 Z= 0.332 Chirality : 0.043 0.181 6760 Planarity : 0.005 0.121 7415 Dihedral : 14.265 177.947 6870 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 1.72 % Allowed : 13.69 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.64 (0.12), residues: 5117 helix: 0.43 (0.12), residues: 1892 sheet: -0.68 (0.19), residues: 704 loop : -0.95 (0.13), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 21 HIS 0.004 0.001 HIS B 246 PHE 0.022 0.002 PHE F 362 TYR 0.027 0.001 TYR J1207 ARG 0.010 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 4.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.5348 (mm) cc_final: 0.4862 (mm) REVERT: B 348 MET cc_start: 0.6247 (mmm) cc_final: 0.5641 (mmm) REVERT: H 140 MET cc_start: 0.7967 (ppp) cc_final: 0.7394 (ppp) REVERT: I 340 MET cc_start: 0.8771 (tmm) cc_final: 0.8276 (tmm) REVERT: I 564 MET cc_start: 0.8446 (mtt) cc_final: 0.8240 (mpp) REVERT: I 880 MET cc_start: 0.8111 (mpp) cc_final: 0.7832 (mpp) REVERT: I 1047 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7323 (m90) REVERT: J 456 MET cc_start: 0.3504 (ttp) cc_final: 0.2616 (ttp) REVERT: J 481 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8531 (tpp) REVERT: J 661 MET cc_start: 0.8982 (ppp) cc_final: 0.8661 (ppp) REVERT: J 1219 GLU cc_start: 0.8614 (pp20) cc_final: 0.8303 (pp20) REVERT: K 29 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.9011 (mp10) REVERT: K 52 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7851 (mm-30) outliers start: 75 outliers final: 51 residues processed: 280 average time/residue: 0.5135 time to fit residues: 250.6708 Evaluate side-chains 267 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 213 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1047 HIS Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 1098 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 416 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 7 optimal weight: 40.0000 chunk 372 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 426 optimal weight: 2.9990 chunk 345 optimal weight: 0.0050 chunk 0 optimal weight: 40.0000 chunk 255 optimal weight: 9.9990 chunk 448 optimal weight: 0.0770 chunk 126 optimal weight: 6.9990 overall best weight: 3.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 415 ASN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS D 347 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 909 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43464 Z= 0.265 Angle : 0.664 14.732 59173 Z= 0.328 Chirality : 0.043 0.202 6760 Planarity : 0.005 0.119 7415 Dihedral : 14.145 177.869 6870 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 2.37 % Allowed : 14.57 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.58 (0.12), residues: 5117 helix: 0.48 (0.12), residues: 1895 sheet: -0.67 (0.19), residues: 698 loop : -0.92 (0.13), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 21 HIS 0.004 0.001 HIS B 246 PHE 0.021 0.002 PHE F 362 TYR 0.025 0.001 TYR J1207 ARG 0.012 0.000 ARG E 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 222 time to evaluate : 4.831 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: B 348 MET cc_start: 0.6143 (mmm) cc_final: 0.5534 (mmm) REVERT: C 348 MET cc_start: 0.5617 (mmm) cc_final: 0.5351 (mmm) REVERT: H 140 MET cc_start: 0.8137 (ppp) cc_final: 0.6935 (ppp) REVERT: I 99 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7971 (pp30) REVERT: I 229 MET cc_start: 0.6845 (mpp) cc_final: 0.6469 (mmm) REVERT: I 275 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: I 340 MET cc_start: 0.8771 (tmm) cc_final: 0.8285 (tmm) REVERT: I 880 MET cc_start: 0.8080 (mpp) cc_final: 0.7769 (mpp) REVERT: J 142 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (mm) REVERT: J 456 MET cc_start: 0.3332 (ttp) cc_final: 0.2587 (ttp) REVERT: J 481 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8462 (tpp) REVERT: J 661 MET cc_start: 0.9012 (ppp) cc_final: 0.8682 (ppp) REVERT: J 1219 GLU cc_start: 0.8628 (pp20) cc_final: 0.8350 (pp20) REVERT: K 29 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.9030 (mp10) REVERT: K 52 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7847 (mm-30) outliers start: 103 outliers final: 64 residues processed: 307 average time/residue: 0.4855 time to fit residues: 261.7688 Evaluate side-chains 281 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 868 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 979 THR Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1098 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 168 optimal weight: 7.9990 chunk 450 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 500 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 43464 Z= 0.361 Angle : 0.724 12.147 59173 Z= 0.361 Chirality : 0.044 0.228 6760 Planarity : 0.005 0.122 7415 Dihedral : 14.160 179.754 6870 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.69 % Rotamer: Outliers : 2.80 % Allowed : 15.92 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.73 (0.12), residues: 5117 helix: 0.34 (0.12), residues: 1888 sheet: -0.72 (0.19), residues: 705 loop : -1.00 (0.13), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP J 21 HIS 0.006 0.002 HIS B 246 PHE 0.023 0.002 PHE I1032 TYR 0.027 0.002 TYR D 105 ARG 0.011 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 211 time to evaluate : 5.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 MET cc_start: 0.6431 (mmm) cc_final: 0.5727 (mmm) REVERT: H 140 MET cc_start: 0.8430 (ppp) cc_final: 0.7649 (ppp) REVERT: H 155 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: I 99 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: I 275 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: I 340 MET cc_start: 0.8812 (tmm) cc_final: 0.8371 (tmm) REVERT: I 564 MET cc_start: 0.8638 (mpp) cc_final: 0.8204 (mpp) REVERT: I 880 MET cc_start: 0.8190 (mpp) cc_final: 0.7829 (mpp) REVERT: J 456 MET cc_start: 0.3347 (ttp) cc_final: 0.2554 (ttp) REVERT: J 481 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8522 (tpp) REVERT: J 661 MET cc_start: 0.8966 (ppp) cc_final: 0.8585 (ppp) REVERT: J 1219 GLU cc_start: 0.8646 (pp20) cc_final: 0.8318 (pp20) REVERT: K 29 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8954 (mp10) REVERT: K 52 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7724 (mm-30) REVERT: K 54 LEU cc_start: 0.3204 (OUTLIER) cc_final: 0.2640 (mt) REVERT: K 88 GLU cc_start: 0.5815 (tp30) cc_final: 0.5585 (pt0) REVERT: K 89 MET cc_start: 0.5986 (tpt) cc_final: 0.5739 (tpt) outliers start: 122 outliers final: 83 residues processed: 312 average time/residue: 0.4975 time to fit residues: 268.1621 Evaluate side-chains 295 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 206 time to evaluate : 4.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 813 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 868 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 968 LEU Chi-restraints excluded: chain I residue 979 THR Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1098 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1349 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 482 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 421 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 498 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 43464 Z= 0.333 Angle : 0.706 12.359 59173 Z= 0.352 Chirality : 0.044 0.253 6760 Planarity : 0.005 0.123 7415 Dihedral : 14.167 177.174 6870 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.13 % Favored : 92.77 % Rotamer: Outliers : 2.73 % Allowed : 16.89 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.71 (0.12), residues: 5117 helix: 0.39 (0.12), residues: 1881 sheet: -0.70 (0.19), residues: 709 loop : -1.01 (0.13), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 21 HIS 0.005 0.001 HIS B 246 PHE 0.022 0.002 PHE I1032 TYR 0.028 0.002 TYR J1207 ARG 0.011 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 218 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 MET cc_start: 0.6465 (mmm) cc_final: 0.5618 (mmm) REVERT: F 97 GLN cc_start: 0.5214 (OUTLIER) cc_final: 0.4488 (pm20) REVERT: H 140 MET cc_start: 0.8385 (ppp) cc_final: 0.7669 (ppp) REVERT: I 91 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8621 (pp30) REVERT: I 99 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8419 (pp30) REVERT: I 275 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: I 340 MET cc_start: 0.8825 (tmm) cc_final: 0.8387 (tmm) REVERT: I 564 MET cc_start: 0.8628 (mpp) cc_final: 0.8061 (mpp) REVERT: I 880 MET cc_start: 0.8152 (mpp) cc_final: 0.7836 (mpp) REVERT: I 1031 ARG cc_start: 0.8301 (mpt180) cc_final: 0.7068 (mmt180) REVERT: J 456 MET cc_start: 0.3407 (ttp) cc_final: 0.2627 (ttp) REVERT: J 481 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8568 (tpp) REVERT: J 661 MET cc_start: 0.8968 (ppp) cc_final: 0.8619 (ppp) REVERT: J 1201 CYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8096 (p) REVERT: J 1204 CYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8248 (m) REVERT: J 1219 GLU cc_start: 0.8669 (pp20) cc_final: 0.8417 (pp20) REVERT: K 29 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8992 (mp10) REVERT: K 43 GLU cc_start: 0.7649 (pp20) cc_final: 0.7432 (pp20) outliers start: 119 outliers final: 83 residues processed: 316 average time/residue: 0.4982 time to fit residues: 273.5503 Evaluate side-chains 297 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 206 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 705 ILE Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 868 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 979 THR Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 839 LEU Chi-restraints excluded: chain J residue 1098 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1201 CYS Chi-restraints excluded: chain J residue 1204 CYS Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1349 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 308 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 391 optimal weight: 40.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 GLN J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 43464 Z= 0.186 Angle : 0.676 14.434 59173 Z= 0.330 Chirality : 0.044 0.369 6760 Planarity : 0.005 0.125 7415 Dihedral : 13.995 177.855 6870 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 1.75 % Allowed : 18.22 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.50 (0.12), residues: 5117 helix: 0.56 (0.12), residues: 1876 sheet: -0.62 (0.20), residues: 702 loop : -0.88 (0.13), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 21 HIS 0.004 0.001 HIS J1367 PHE 0.021 0.001 PHE F 362 TYR 0.022 0.001 TYR J1207 ARG 0.011 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 228 time to evaluate : 4.659 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: F 405 MET cc_start: 0.3982 (ppp) cc_final: 0.3666 (ppp) REVERT: H 140 MET cc_start: 0.8316 (ppp) cc_final: 0.7620 (ppp) REVERT: H 194 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8313 (ttmt) REVERT: I 91 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8652 (pp30) REVERT: I 99 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8086 (pp30) REVERT: I 275 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8264 (m-10) REVERT: I 340 MET cc_start: 0.8786 (tmm) cc_final: 0.8315 (tmm) REVERT: I 880 MET cc_start: 0.7989 (mpp) cc_final: 0.7743 (mpp) REVERT: I 1031 ARG cc_start: 0.8146 (mpt180) cc_final: 0.6891 (mmt180) REVERT: J 125 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8605 (pp30) REVERT: J 456 MET cc_start: 0.3276 (ttp) cc_final: 0.2579 (ttp) REVERT: J 481 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8555 (tpp) REVERT: J 661 MET cc_start: 0.8960 (ppp) cc_final: 0.8646 (ppp) REVERT: J 902 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8473 (pp) REVERT: J 1219 GLU cc_start: 0.8613 (pp20) cc_final: 0.8387 (pp20) REVERT: K 29 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8855 (mp10) REVERT: K 52 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7757 (mm-30) outliers start: 76 outliers final: 57 residues processed: 287 average time/residue: 0.5065 time to fit residues: 252.9414 Evaluate side-chains 276 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 4.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain J residue 60 CYS Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 453 optimal weight: 1.9990 chunk 477 optimal weight: 9.9990 chunk 435 optimal weight: 0.4980 chunk 464 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 419 optimal weight: 4.9990 chunk 439 optimal weight: 0.7980 chunk 462 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43464 Z= 0.203 Angle : 0.675 18.261 59173 Z= 0.328 Chirality : 0.043 0.281 6760 Planarity : 0.005 0.127 7415 Dihedral : 13.904 179.144 6870 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 1.70 % Allowed : 18.34 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.44 (0.12), residues: 5117 helix: 0.59 (0.12), residues: 1866 sheet: -0.58 (0.19), residues: 718 loop : -0.82 (0.13), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP J 21 HIS 0.006 0.001 HIS I1047 PHE 0.020 0.001 PHE F 362 TYR 0.046 0.001 TYR J 868 ARG 0.009 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 5.364 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: F 97 GLN cc_start: 0.4906 (OUTLIER) cc_final: 0.4322 (pm20) REVERT: F 405 MET cc_start: 0.3970 (ppp) cc_final: 0.3739 (ppp) REVERT: H 140 MET cc_start: 0.8264 (ppp) cc_final: 0.7569 (ppp) REVERT: H 194 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8336 (ttmt) REVERT: I 91 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8603 (pp30) REVERT: I 99 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8035 (pp30) REVERT: I 275 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: I 340 MET cc_start: 0.8769 (tmm) cc_final: 0.8315 (tmm) REVERT: I 880 MET cc_start: 0.8014 (mpp) cc_final: 0.7798 (mpp) REVERT: I 1031 ARG cc_start: 0.8195 (mpt180) cc_final: 0.6988 (mmt180) REVERT: J 456 MET cc_start: 0.3454 (ttp) cc_final: 0.2759 (ttp) REVERT: J 481 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8567 (tpp) REVERT: J 661 MET cc_start: 0.8945 (ppp) cc_final: 0.8615 (ppp) REVERT: J 902 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8449 (pp) REVERT: J 1219 GLU cc_start: 0.8614 (pp20) cc_final: 0.8384 (pp20) REVERT: K 29 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8778 (mp10) REVERT: K 88 GLU cc_start: 0.5797 (tp30) cc_final: 0.5461 (pt0) outliers start: 74 outliers final: 61 residues processed: 280 average time/residue: 0.5034 time to fit residues: 247.5868 Evaluate side-chains 278 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 210 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain J residue 60 CYS Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 839 LEU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 304 optimal weight: 0.1980 chunk 491 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 chunk 515 optimal weight: 10.0000 chunk 474 optimal weight: 0.0870 chunk 410 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43464 Z= 0.181 Angle : 0.665 14.353 59173 Z= 0.323 Chirality : 0.043 0.326 6760 Planarity : 0.005 0.126 7415 Dihedral : 13.801 179.694 6870 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 1.68 % Allowed : 18.41 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.39 (0.12), residues: 5117 helix: 0.60 (0.12), residues: 1872 sheet: -0.50 (0.20), residues: 705 loop : -0.78 (0.13), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP J 21 HIS 0.004 0.001 HIS B 246 PHE 0.021 0.001 PHE F 362 TYR 0.039 0.001 TYR J 868 ARG 0.008 0.000 ARG E 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 218 time to evaluate : 4.856 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: F 348 MET cc_start: 0.4778 (mmm) cc_final: 0.4284 (mmm) REVERT: G 123 MET cc_start: 0.8339 (mmm) cc_final: 0.7982 (mpp) REVERT: H 140 MET cc_start: 0.8449 (ppp) cc_final: 0.7183 (ppp) REVERT: H 194 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8356 (ttmt) REVERT: I 91 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8598 (pp30) REVERT: I 99 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: I 275 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: I 321 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: I 340 MET cc_start: 0.8759 (tmm) cc_final: 0.8294 (tmm) REVERT: I 1031 ARG cc_start: 0.8171 (mpt180) cc_final: 0.7019 (mmt180) REVERT: J 456 MET cc_start: 0.3439 (ttp) cc_final: 0.2682 (ttp) REVERT: J 481 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8547 (tpp) REVERT: J 661 MET cc_start: 0.8970 (ppp) cc_final: 0.8618 (ppp) REVERT: J 902 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8436 (pp) REVERT: J 1219 GLU cc_start: 0.8603 (pp20) cc_final: 0.8376 (pp20) REVERT: K 29 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8691 (mp10) REVERT: K 52 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7812 (mm-30) REVERT: K 88 GLU cc_start: 0.5966 (tp30) cc_final: 0.5415 (pt0) outliers start: 73 outliers final: 56 residues processed: 280 average time/residue: 0.4988 time to fit residues: 245.0689 Evaluate side-chains 274 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 211 time to evaluate : 5.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain J residue 60 CYS Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 325 optimal weight: 8.9990 chunk 436 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 378 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 410 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1037 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.059657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.043824 restraints weight = 306292.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045050 restraints weight = 180528.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.045859 restraints weight = 128704.774| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 43464 Z= 0.188 Angle : 0.665 13.916 59173 Z= 0.322 Chirality : 0.043 0.318 6760 Planarity : 0.005 0.127 7415 Dihedral : 13.712 176.192 6870 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 1.63 % Allowed : 18.61 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.33 (0.12), residues: 5117 helix: 0.65 (0.12), residues: 1871 sheet: -0.48 (0.20), residues: 699 loop : -0.75 (0.13), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP J 21 HIS 0.007 0.001 HIS A 246 PHE 0.029 0.001 PHE A 307 TYR 0.037 0.001 TYR J 868 ARG 0.009 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7230.09 seconds wall clock time: 134 minutes 6.32 seconds (8046.32 seconds total)