Starting phenix.real_space_refine on Thu May 22 07:57:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.map" model { file = "/net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wiv_37569/05_2025/8wiv_37569.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 14366 2.51 5 N 3867 2.21 5 O 4315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22622 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3133 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 5 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4667 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 26, 'TRANS': 575} Chain breaks: 4 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4757 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 29, 'TRANS': 600} Chain breaks: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 163 Chain: "O" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5002 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "L" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4935 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 30, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.91, per 1000 atoms: 0.57 Number of scatterers: 22622 At special positions: 0 Unit cell: (118.336, 137.7, 151.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 4 11.99 O 4315 8.00 N 3867 7.00 C 14366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 17 sheets defined 34.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.365A pdb=" N VAL A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.542A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.624A pdb=" N GLN A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.922A pdb=" N ALA A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.765A pdb=" N GLY A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.509A pdb=" N ASN A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.607A pdb=" N GLU A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.710A pdb=" N TRP A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.761A pdb=" N THR A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.417A pdb=" N ASP A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.918A pdb=" N GLU A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 519 through 528 removed outlier: 3.582A pdb=" N HIS A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.792A pdb=" N MET A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 122 through 131 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.740A pdb=" N THR D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 248 through 269 removed outlier: 3.632A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.826A pdb=" N LEU D 279 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.514A pdb=" N LEU D 364 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 365 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.974A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 423 through 439 removed outlier: 3.844A pdb=" N ILE D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 502 through 507 Processing helix chain 'D' and resid 519 through 528 removed outlier: 3.658A pdb=" N ARG D 523 " --> pdb=" O ASN D 519 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N HIS D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.590A pdb=" N THR D 543 " --> pdb=" O MET D 540 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 544 " --> pdb=" O LEU D 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 544' Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.759A pdb=" N ASN D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.298A pdb=" N VAL D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 597 " --> pdb=" O TYR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.710A pdb=" N GLU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 removed outlier: 3.785A pdb=" N GLN D 686 " --> pdb=" O PHE D 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 687 " --> pdb=" O PHE D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 691 removed outlier: 4.459A pdb=" N TYR D 691 " --> pdb=" O LYS D 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 688 through 691' Processing helix chain 'M' and resid 78 through 82 removed outlier: 4.149A pdb=" N GLU M 81 " --> pdb=" O LYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'M' and resid 155 through 161 Processing helix chain 'M' and resid 173 through 185 removed outlier: 3.597A pdb=" N THR M 178 " --> pdb=" O SER M 174 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER M 179 " --> pdb=" O THR M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 233 Processing helix chain 'M' and resid 234 through 240 Processing helix chain 'M' and resid 248 through 269 removed outlier: 3.904A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA M 253 " --> pdb=" O SER M 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 299 removed outlier: 3.636A pdb=" N LEU M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 315 Processing helix chain 'M' and resid 360 through 371 removed outlier: 3.518A pdb=" N SER M 369 " --> pdb=" O GLU M 365 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 370 " --> pdb=" O GLY M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 375 removed outlier: 5.985A pdb=" N ARG M 375 " --> pdb=" O LYS M 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 372 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 396 through 405 removed outlier: 4.111A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 422 No H-bonds generated for 'chain 'M' and resid 420 through 422' Processing helix chain 'M' and resid 423 through 441 removed outlier: 3.633A pdb=" N LEU M 435 " --> pdb=" O LEU M 431 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP M 441 " --> pdb=" O ASP M 437 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 464 removed outlier: 3.908A pdb=" N THR M 463 " --> pdb=" O GLU M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 484 Processing helix chain 'M' and resid 485 through 487 No H-bonds generated for 'chain 'M' and resid 485 through 487' Processing helix chain 'M' and resid 497 through 501 Processing helix chain 'M' and resid 502 through 508 Processing helix chain 'M' and resid 519 through 528 removed outlier: 3.766A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN M 524 " --> pdb=" O SER M 520 " (cutoff:3.500A) Processing helix chain 'M' and resid 537 through 544 removed outlier: 3.833A pdb=" N MET M 540 " --> pdb=" O LEU M 537 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU M 541 " --> pdb=" O MET M 538 " (cutoff:3.500A) Proline residue: M 542 - end of helix No H-bonds generated for 'chain 'M' and resid 537 through 544' Processing helix chain 'M' and resid 579 through 586 removed outlier: 3.976A pdb=" N ASN M 586 " --> pdb=" O ALA M 582 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 4.251A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR M 598 " --> pdb=" O LYS M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 655 through 657 No H-bonds generated for 'chain 'M' and resid 655 through 657' Processing helix chain 'M' and resid 667 through 677 removed outlier: 3.801A pdb=" N GLU M 677 " --> pdb=" O LEU M 673 " (cutoff:3.500A) Processing helix chain 'M' and resid 682 through 687 removed outlier: 4.361A pdb=" N GLN M 686 " --> pdb=" O PHE M 682 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 83 Processing helix chain 'O' and resid 122 through 131 Processing helix chain 'O' and resid 155 through 161 Processing helix chain 'O' and resid 168 through 171 removed outlier: 3.621A pdb=" N SER O 171 " --> pdb=" O SER O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 168 through 171' Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.512A pdb=" N THR O 176 " --> pdb=" O GLY O 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER O 185 " --> pdb=" O LEU O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 243 removed outlier: 3.779A pdb=" N PHE O 238 " --> pdb=" O THR O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 268 removed outlier: 3.683A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG O 268 " --> pdb=" O GLN O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 301 Processing helix chain 'O' and resid 311 through 315 removed outlier: 3.501A pdb=" N GLU O 315 " --> pdb=" O GLU O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 373 removed outlier: 3.631A pdb=" N LEU O 370 " --> pdb=" O GLY O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 381 Processing helix chain 'O' and resid 396 through 405 removed outlier: 3.685A pdb=" N LEU O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 423 through 442 removed outlier: 3.666A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY O 429 " --> pdb=" O ASP O 425 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE O 432 " --> pdb=" O ILE O 428 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER O 442 " --> pdb=" O SER O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 484 Processing helix chain 'O' and resid 497 through 501 Processing helix chain 'O' and resid 502 through 508 removed outlier: 3.814A pdb=" N GLN O 508 " --> pdb=" O THR O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 528 removed outlier: 3.526A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN O 524 " --> pdb=" O SER O 520 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS O 525 " --> pdb=" O SER O 521 " (cutoff:3.500A) Processing helix chain 'O' and resid 579 through 585 removed outlier: 3.587A pdb=" N SER O 585 " --> pdb=" O THR O 581 " (cutoff:3.500A) Processing helix chain 'O' and resid 592 through 603 removed outlier: 4.340A pdb=" N VAL O 596 " --> pdb=" O ASP O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 677 removed outlier: 3.862A pdb=" N HIS O 670 " --> pdb=" O PRO O 666 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR O 671 " --> pdb=" O GLU O 667 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU O 672 " --> pdb=" O THR O 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 681 through 686 Processing helix chain 'L' and resid 122 through 131 Processing helix chain 'L' and resid 172 through 184 removed outlier: 4.183A pdb=" N SER L 179 " --> pdb=" O THR L 175 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE L 180 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE L 184 " --> pdb=" O ILE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 244 Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.792A pdb=" N ILE L 255 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP L 256 " --> pdb=" O ASN L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 301 Processing helix chain 'L' and resid 311 through 315 Processing helix chain 'L' and resid 360 through 373 removed outlier: 3.558A pdb=" N LEU L 370 " --> pdb=" O GLY L 366 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 371 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS L 372 " --> pdb=" O ALA L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 396 through 406 removed outlier: 3.945A pdb=" N LEU L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 442 removed outlier: 3.689A pdb=" N ILE L 428 " --> pdb=" O LEU L 424 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY L 429 " --> pdb=" O ASP L 425 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 4.037A pdb=" N THR L 463 " --> pdb=" O GLU L 460 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU L 465 " --> pdb=" O HIS L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 488 removed outlier: 3.784A pdb=" N ILE L 480 " --> pdb=" O GLY L 476 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG L 485 " --> pdb=" O VAL L 481 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS L 486 " --> pdb=" O LYS L 482 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR L 487 " --> pdb=" O GLU L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 501 Processing helix chain 'L' and resid 502 through 507 Processing helix chain 'L' and resid 519 through 527 removed outlier: 4.047A pdb=" N HIS L 525 " --> pdb=" O SER L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 585 removed outlier: 3.782A pdb=" N SER L 585 " --> pdb=" O THR L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 603 removed outlier: 3.907A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 657 No H-bonds generated for 'chain 'L' and resid 655 through 657' Processing helix chain 'L' and resid 667 through 676 removed outlier: 3.764A pdb=" N THR L 671 " --> pdb=" O GLU L 667 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 687 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.262A pdb=" N ARG A 26 " --> pdb=" O GLN A 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 29 current: chain 'A' and resid 62 through 70 removed outlier: 6.976A pdb=" N ASN A 62 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU A 97 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER A 91 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL A 70 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N TRP A 89 " --> pdb=" O VAL A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 106 current: chain 'D' and resid 25 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 61 through 71 removed outlier: 7.028A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 106 current: chain 'O' and resid 61 through 71 removed outlier: 6.968A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TRP O 89 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 6.213A pdb=" N ALA A 151 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 456 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 494 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 458 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 150 through 153 removed outlier: 4.997A pdb=" N GLY D 141 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D 153 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER D 139 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 142 " --> pdb=" O ILE D 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.690A pdb=" N LEU D 224 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 213 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP D 415 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 215 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 195 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE D 414 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 197 " --> pdb=" O PHE D 414 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE D 196 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 638 through 641 removed outlier: 3.971A pdb=" N SER D 640 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 692 " --> pdb=" O TYR D 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 15 through 19 removed outlier: 6.792A pdb=" N ARG M 26 " --> pdb=" O GLN M 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 54 through 58 removed outlier: 3.886A pdb=" N GLY M 65 " --> pdb=" O VAL M 54 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN M 62 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE M 64 " --> pdb=" O GLY M 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 150 through 153 removed outlier: 3.964A pdb=" N GLY M 141 " --> pdb=" O ALA M 151 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL M 153 " --> pdb=" O SER M 139 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER M 139 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU M 454 " --> pdb=" O GLY M 490 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N MET M 492 " --> pdb=" O LEU M 454 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL M 456 " --> pdb=" O MET M 492 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL M 494 " --> pdb=" O VAL M 456 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU M 458 " --> pdb=" O VAL M 494 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU M 224 " --> pdb=" O VAL M 214 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS M 216 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 617 through 618 removed outlier: 3.584A pdb=" N LEU M 617 " --> pdb=" O ILE M 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE M 641 " --> pdb=" O LEU M 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 19 through 20 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 19 through 20 current: chain 'L' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 29 current: chain 'L' and resid 61 through 71 removed outlier: 6.664A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL L 70 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP L 89 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 137 through 139 Processing sheet with id=AB3, first strand: chain 'O' and resid 458 through 459 removed outlier: 6.542A pdb=" N LEU O 458 " --> pdb=" O VAL O 494 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA O 164 " --> pdb=" O PHE O 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 195 through 199 removed outlier: 3.511A pdb=" N SER O 412 " --> pdb=" O ILE O 195 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS O 213 " --> pdb=" O ILE O 413 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP O 415 " --> pdb=" O LYS O 213 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR O 215 " --> pdb=" O ASP O 415 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 617 through 618 removed outlier: 4.186A pdb=" N SER O 640 " --> pdb=" O GLU O 653 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 153 removed outlier: 6.756A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN L 142 " --> pdb=" O ILE L 563 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL L 456 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL L 494 " --> pdb=" O VAL L 456 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU L 458 " --> pdb=" O VAL L 494 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE L 195 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE L 414 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL L 197 " --> pdb=" O PHE L 414 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS L 213 " --> pdb=" O ILE L 411 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE L 413 " --> pdb=" O LYS L 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 616 through 618 removed outlier: 3.562A pdb=" N LEU L 617 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER L 640 " --> pdb=" O GLU L 653 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU L 653 " --> pdb=" O SER L 640 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU L 651 " --> pdb=" O GLY L 642 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG L 692 " --> pdb=" O TYR L 663 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7466 1.35 - 1.49: 5727 1.49 - 1.63: 9712 1.63 - 1.77: 32 1.77 - 1.92: 102 Bond restraints: 23039 Sorted by residual: bond pdb=" C3' AGS O 701 " pdb=" C4' AGS O 701 " ideal model delta sigma weight residual 1.526 1.272 0.254 1.10e-02 8.26e+03 5.34e+02 bond pdb=" C3' AGS L 701 " pdb=" C4' AGS L 701 " ideal model delta sigma weight residual 1.526 1.272 0.254 1.10e-02 8.26e+03 5.33e+02 bond pdb=" C3' AGS D 702 " pdb=" C4' AGS D 702 " ideal model delta sigma weight residual 1.526 1.273 0.253 1.10e-02 8.26e+03 5.29e+02 bond pdb=" C3' AGS M 701 " pdb=" C4' AGS M 701 " ideal model delta sigma weight residual 1.526 1.274 0.252 1.10e-02 8.26e+03 5.24e+02 bond pdb=" C1' AGS M 701 " pdb=" C2' AGS M 701 " ideal model delta sigma weight residual 1.530 1.273 0.257 1.30e-02 5.92e+03 3.90e+02 ... (remaining 23034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30961 2.61 - 5.22: 272 5.22 - 7.83: 22 7.83 - 10.43: 8 10.43 - 13.04: 8 Bond angle restraints: 31271 Sorted by residual: angle pdb=" C5 AGS L 701 " pdb=" N7 AGS L 701 " pdb=" C8 AGS L 701 " ideal model delta sigma weight residual 103.67 108.19 -4.52 4.26e-01 5.51e+00 1.13e+02 angle pdb=" N1 AGS M 701 " pdb=" C2 AGS M 701 " pdb=" N3 AGS M 701 " ideal model delta sigma weight residual 128.80 119.98 8.82 8.41e-01 1.41e+00 1.10e+02 angle pdb=" N1 AGS O 701 " pdb=" C2 AGS O 701 " pdb=" N3 AGS O 701 " ideal model delta sigma weight residual 128.80 120.02 8.78 8.41e-01 1.41e+00 1.09e+02 angle pdb=" N1 AGS D 702 " pdb=" C2 AGS D 702 " pdb=" N3 AGS D 702 " ideal model delta sigma weight residual 128.80 120.07 8.73 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS L 701 " pdb=" C2 AGS L 701 " pdb=" N3 AGS L 701 " ideal model delta sigma weight residual 128.80 120.13 8.67 8.41e-01 1.41e+00 1.06e+02 ... (remaining 31266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 13222 23.78 - 47.55: 555 47.55 - 71.33: 50 71.33 - 95.11: 14 95.11 - 118.89: 2 Dihedral angle restraints: 13843 sinusoidal: 5444 harmonic: 8399 Sorted by residual: dihedral pdb=" CA ARG L 161 " pdb=" C ARG L 161 " pdb=" N HIS L 162 " pdb=" CA HIS L 162 " ideal model delta harmonic sigma weight residual 180.00 151.83 28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA MET A 560 " pdb=" C MET A 560 " pdb=" N ARG A 561 " pdb=" CA ARG A 561 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA HIS L 679 " pdb=" C HIS L 679 " pdb=" N GLY L 680 " pdb=" CA GLY L 680 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 13840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2815 0.048 - 0.095: 561 0.095 - 0.143: 230 0.143 - 0.191: 10 0.191 - 0.238: 5 Chirality restraints: 3621 Sorted by residual: chirality pdb=" C2' AGS D 702 " pdb=" C1' AGS D 702 " pdb=" C3' AGS D 702 " pdb=" O2' AGS D 702 " both_signs ideal model delta sigma weight residual False -2.67 -2.44 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2' AGS L 701 " pdb=" C1' AGS L 701 " pdb=" C3' AGS L 701 " pdb=" O2' AGS L 701 " both_signs ideal model delta sigma weight residual False -2.67 -2.44 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2' AGS O 701 " pdb=" C1' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" O2' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.67 -2.45 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3618 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 441 " 0.025 2.00e-02 2.50e+03 1.88e-02 8.80e+00 pdb=" CG TRP D 441 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 441 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 441 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 441 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 441 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 441 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 441 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 441 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 441 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 56 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO A 57 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 123 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO D 124 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.031 5.00e-02 4.00e+02 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 12 2.01 - 2.73: 1825 2.73 - 3.45: 33091 3.45 - 4.18: 49070 4.18 - 4.90: 89246 Nonbonded interactions: 173244 Sorted by model distance: nonbonded pdb=" OE2 GLU O 459 " pdb="MG MG O 702 " model vdw 1.285 2.170 nonbonded pdb=" O3G AGS M 701 " pdb="MG MG M 702 " model vdw 1.565 2.170 nonbonded pdb=" OH TYR D 204 " pdb=" OE2 GLU D 459 " model vdw 1.805 3.040 nonbonded pdb=" O ARG L 161 " pdb=" ND1 HIS L 162 " model vdw 1.894 3.120 nonbonded pdb=" OG SER D 174 " pdb="MG MG D 701 " model vdw 1.937 2.170 ... (remaining 173239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 23 or (resid 24 through 27 and (name N or na \ me CA or name C or name O or name CB )) or resid 28 through 30 or resid 48 throu \ gh 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or r \ esid 61 through 67 or (resid 68 and (name N or name CA or name C or name O or na \ me CB )) or resid 69 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 80 or (resid 81 through 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 or (resid 85 and (name \ N or name CA or name C or name O or name CB )) or resid 86 or (resid 87 through \ 88 and (name N or name CA or name C or name O or name CB )) or resid 89 through \ 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or res \ id 94 through 100 or (resid 101 and (name N or name CA or name C or name O or na \ me CB )) or resid 102 through 122 or (resid 123 and (name N or name CA or name C \ or name O or name CB )) or resid 124 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 129 or (resid 130 \ and (name N or name CA or name C or name O or name CB )) or resid 131 or (resid \ 132 through 133 and (name N or name CA or name C or name O or name CB )) or resi \ d 134 or (resid 135 through 136 and (name N or name CA or name C or name O or na \ me CB )) or resid 137 through 153 or (resid 154 and (name N or name CA or name C \ or name O or name CB )) or resid 155 through 544 or (resid 545 and (name N or n \ ame CA or name C or name O or name CB )) or resid 546 through 553 or (resid 554 \ and (name N or name CA or name C or name O or name CB )) or resid 555 through 55 \ 6 or (resid 557 and (name N or name CA or name C or name O or name CB )) or resi \ d 558 through 561 or (resid 562 and (name N or name CA or name C or name O or na \ me CB )) or resid 563 through 570 or (resid 571 and (name N or name CA or name C \ or name O or name CB )) or resid 572 through 652 or (resid 653 and (name N or n \ ame CA or name C or name O or name CB )) or resid 654 through 655 or (resid 656 \ and (name N or name CA or name C or name O or name CB )) or resid 657 through 67 \ 1 or (resid 672 through 673 and (name N or name CA or name C or name O or name C \ B )) or resid 674 through 677 or (resid 678 through 679 and (name N or name CA o \ r name C or name O or name CB )) or resid 680 or (resid 681 through 682 and (nam \ e N or name CA or name C or name O or name CB )) or resid 683 through 684 or (re \ sid 685 through 686 and (name N or name CA or name C or name O or name CB )) or \ resid 687 through 696)) selection = (chain 'L' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 23 or (resid 24 through 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 or (resid 29 through 30 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 59 or (resid 60 and \ (name N or name CA or name C or name O or name CB )) or resid 61 through 77 or ( \ resid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 th \ rough 80 or (resid 81 through 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 or (resid 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 or (resid 87 through 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 through 92 or (resid 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 100 or (resid 101 and \ (name N or name CA or name C or name O or name CB )) or resid 102 through 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 126 or (resid 127 and (name N or name CA or name C or name O or name C \ B )) or resid 128 through 129 or (resid 130 and (name N or name CA or name C or \ name O or name CB )) or resid 131 or (resid 132 through 133 and (name N or name \ CA or name C or name O or name CB )) or resid 134 or (resid 135 through 136 and \ (name N or name CA or name C or name O or name CB )) or resid 137 through 269 or \ (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 1 through 302 or resid 332 through 336 or resid 359 through 406 or (resid 407 an \ d (name N or name CA or name C or name O or name CB )) or resid 408 through 544 \ or (resid 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 553 or (resid 554 and (name N or name CA or name C or name O or name \ CB )) or resid 555 through 556 or (resid 557 and (name N or name CA or name C o \ r name O or name CB )) or resid 558 through 561 or (resid 562 and (name N or nam \ e CA or name C or name O or name CB )) or resid 563 through 570 or (resid 571 an \ d (name N or name CA or name C or name O or name CB )) or resid 572 through 593 \ or (resid 594 through 595 and (name N or name CA or name C or name O or name CB \ )) or resid 596 through 607 or resid 637 through 652 or (resid 653 and (name N o \ r name CA or name C or name O or name CB )) or resid 654 through 655 or (resid 6 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 657 through \ 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) or r \ esid 683 or (resid 684 through 686 and (name N or name CA or name C or name O or \ name CB )) or resid 687 through 689 or (resid 690 through 691 and (name N or na \ me CA or name C or name O or name CB )) or resid 692 through 696)) selection = (chain 'M' and (resid 11 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 100 or ( \ resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 126 or (resid 127 and (name N or name CA or name C or name O or name CB \ )) or resid 128 through 153 or (resid 154 and (name N or name CA or name C or na \ me O or name CB )) or resid 155 through 269 or (resid 270 and (name N or name CA \ or name C or name O or name CB )) or resid 271 through 302 or resid 332 through \ 336 or resid 359 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 561 or (resid 562 and (name N or name \ CA or name C or name O or name CB )) or resid 563 through 593 or (resid 594 thro \ ugh 595 and (name N or name CA or name C or name O or name CB )) or resid 596 th \ rough 607 or resid 637 through 671 or (resid 672 through 673 and (name N or name \ CA or name C or name O or name CB )) or resid 674 through 676 or (resid 677 thr \ ough 679 and (name N or name CA or name C or name O or name CB )) or resid 680 o \ r (resid 681 through 682 and (name N or name CA or name C or name O or name CB ) \ ) or resid 683 or (resid 684 through 686 and (name N or name CA or name C or nam \ e O or name CB )) or resid 687 or (resid 688 and (name N or name CA or name C or \ name O or name CB )) or resid 689 or (resid 690 through 691 and (name N or name \ CA or name C or name O or name CB )) or resid 692 through 696)) selection = (chain 'O' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 23 or (resid 24 through 27 and (name N or na \ me CA or name C or name O or name CB )) or resid 28 or (resid 29 through 30 and \ (name N or name CA or name C or name O or name CB )) or resid 48 through 67 or ( \ resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 th \ rough 80 or (resid 81 through 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 through 92 or (resid 93 and (name N or name CA or name C o \ r name O or name CB )) or resid 94 through 129 or (resid 130 and (name N or name \ CA or name C or name O or name CB )) or resid 131 or (resid 132 through 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 135 o \ r (resid 136 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 37 through 153 or (resid 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 269 or (resid 270 and (name N or name CA or name C or \ name O or name CB )) or resid 271 through 302 or resid 332 through 336 or resid \ 359 through 406 or (resid 407 and (name N or name CA or name C or name O or nam \ e CB )) or resid 408 through 544 or (resid 545 and (name N or name CA or name C \ or name O or name CB )) or resid 546 through 553 or (resid 554 and (name N or na \ me CA or name C or name O or name CB )) or resid 555 through 556 or (resid 557 a \ nd (name N or name CA or name C or name O or name CB )) or resid 558 through 593 \ or (resid 594 through 595 and (name N or name CA or name C or name O or name CB \ )) or resid 596 through 607 or resid 637 through 652 or (resid 653 and (name N \ or name CA or name C or name O or name CB )) or resid 654 through 655 or (resid \ 656 and (name N or name CA or name C or name O or name CB )) or resid 657 throug \ h 671 or (resid 672 through 673 and (name N or name CA or name C or name O or na \ me CB )) or resid 674 through 676 or (resid 677 through 679 and (name N or name \ CA or name C or name O or name CB )) or resid 680 or (resid 681 through 682 and \ (name N or name CA or name C or name O or name CB )) or resid 683 or (resid 684 \ through 686 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 7 or (resid 688 and (name N or name CA or name C or name O or name CB )) or resi \ d 689 or (resid 690 through 691 and (name N or name CA or name C or name O or na \ me CB )) or resid 692 through 696)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 47.830 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.008 0.304 23040 Z= 0.591 Angle : 0.646 13.043 31271 Z= 0.428 Chirality : 0.045 0.238 3621 Planarity : 0.005 0.063 3983 Dihedral : 12.550 118.885 8457 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2896 helix: -0.73 (0.18), residues: 799 sheet: -1.85 (0.24), residues: 442 loop : -1.26 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 441 HIS 0.005 0.001 HIS A 162 PHE 0.023 0.002 PHE O 534 TYR 0.033 0.001 TYR O 662 ARG 0.007 0.001 ARG L 161 Details of bonding type rmsd hydrogen bonds : bond 0.26654 ( 671) hydrogen bonds : angle 9.34894 ( 1881) covalent geometry : bond 0.00756 (23039) covalent geometry : angle 0.64609 (31271) Misc. bond : bond 0.30433 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7728 (p) cc_final: 0.7505 (m) REVERT: M 641 ILE cc_start: 0.7292 (tt) cc_final: 0.6632 (mt) REVERT: O 500 GLU cc_start: 0.7603 (tp30) cc_final: 0.7316 (tp30) REVERT: O 538 MET cc_start: 0.7496 (mmm) cc_final: 0.6982 (mmt) REVERT: O 540 MET cc_start: 0.6447 (ptp) cc_final: 0.6115 (ptp) REVERT: O 651 GLU cc_start: 0.7097 (pt0) cc_final: 0.6772 (pt0) REVERT: L 560 MET cc_start: 0.7323 (ptm) cc_final: 0.6684 (ptp) REVERT: L 686 GLN cc_start: 0.8010 (mt0) cc_final: 0.7417 (mt0) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.3315 time to fit residues: 194.1194 Evaluate side-chains 257 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 88 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 670 HIS L 119 HIS L 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.185868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.153640 restraints weight = 38222.798| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.13 r_work: 0.3878 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23040 Z= 0.144 Angle : 0.629 8.946 31271 Z= 0.325 Chirality : 0.048 0.204 3621 Planarity : 0.004 0.046 3983 Dihedral : 7.280 125.434 3243 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.16 % Allowed : 8.56 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2896 helix: -0.33 (0.17), residues: 870 sheet: -1.51 (0.25), residues: 428 loop : -1.07 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 404 HIS 0.014 0.001 HIS A 162 PHE 0.019 0.002 PHE A 243 TYR 0.021 0.001 TYR O 662 ARG 0.006 0.001 ARG M 55 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 671) hydrogen bonds : angle 6.17619 ( 1881) covalent geometry : bond 0.00329 (23039) covalent geometry : angle 0.62915 (31271) Misc. bond : bond 0.00254 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.5701 (ttpp) cc_final: 0.4552 (tptt) REVERT: A 457 VAL cc_start: 0.7587 (p) cc_final: 0.7240 (m) REVERT: D 247 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6761 (mm-30) REVERT: M 492 MET cc_start: 0.5350 (tpp) cc_final: 0.4787 (tpp) REVERT: M 641 ILE cc_start: 0.7765 (tt) cc_final: 0.7372 (mt) REVERT: O 332 LEU cc_start: 0.8506 (tp) cc_final: 0.8293 (tp) REVERT: O 500 GLU cc_start: 0.7746 (tp30) cc_final: 0.7532 (tp30) REVERT: L 332 LEU cc_start: 0.7918 (mt) cc_final: 0.7496 (mp) REVERT: L 464 TYR cc_start: 0.8302 (m-80) cc_final: 0.7934 (m-80) REVERT: L 532 ASP cc_start: 0.6777 (t0) cc_final: 0.6461 (t0) outliers start: 28 outliers final: 15 residues processed: 322 average time/residue: 0.3187 time to fit residues: 162.0920 Evaluate side-chains 260 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 285 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 252 ASN L 670 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.148863 restraints weight = 38080.184| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.35 r_work: 0.3817 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23040 Z= 0.191 Angle : 0.632 10.616 31271 Z= 0.322 Chirality : 0.048 0.192 3621 Planarity : 0.004 0.051 3983 Dihedral : 7.487 123.042 3243 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.32 % Allowed : 11.49 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 2896 helix: -0.26 (0.18), residues: 857 sheet: -1.40 (0.25), residues: 421 loop : -1.12 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 231 HIS 0.011 0.001 HIS L 162 PHE 0.026 0.002 PHE D 378 TYR 0.022 0.002 TYR A 130 ARG 0.005 0.001 ARG L 588 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 671) hydrogen bonds : angle 5.85756 ( 1881) covalent geometry : bond 0.00470 (23039) covalent geometry : angle 0.63195 (31271) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7523 (p) cc_final: 0.7100 (m) REVERT: M 377 GLU cc_start: 0.7395 (pt0) cc_final: 0.7131 (mm-30) REVERT: M 492 MET cc_start: 0.5224 (tpp) cc_final: 0.4698 (tpp) REVERT: M 592 ASP cc_start: 0.7955 (t0) cc_final: 0.7131 (t0) REVERT: M 595 GLU cc_start: 0.6948 (mp0) cc_final: 0.6442 (mp0) REVERT: M 641 ILE cc_start: 0.7731 (tt) cc_final: 0.7335 (mt) REVERT: O 200 ILE cc_start: 0.8295 (mm) cc_final: 0.8015 (mm) REVERT: O 332 LEU cc_start: 0.8532 (tp) cc_final: 0.8269 (tp) REVERT: O 500 GLU cc_start: 0.7875 (tp30) cc_final: 0.7502 (tp30) REVERT: O 560 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.5873 (ptp) REVERT: L 464 TYR cc_start: 0.8341 (m-80) cc_final: 0.8024 (m-80) REVERT: L 532 ASP cc_start: 0.7028 (t0) cc_final: 0.6781 (t0) REVERT: L 592 ASP cc_start: 0.7590 (t0) cc_final: 0.7379 (t0) outliers start: 56 outliers final: 39 residues processed: 298 average time/residue: 0.3201 time to fit residues: 153.3830 Evaluate side-chains 273 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 540 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 517 MET Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 530 VAL Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 150 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 231 optimal weight: 0.0070 chunk 147 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS O 49 GLN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 GLN O 689 ASN L 18 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149887 restraints weight = 38672.653| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.25 r_work: 0.3849 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23040 Z= 0.128 Angle : 0.563 9.233 31271 Z= 0.288 Chirality : 0.046 0.193 3621 Planarity : 0.004 0.047 3983 Dihedral : 7.372 123.942 3243 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.77 % Allowed : 13.27 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 2896 helix: -0.04 (0.18), residues: 855 sheet: -1.23 (0.25), residues: 422 loop : -1.04 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 231 HIS 0.007 0.001 HIS L 162 PHE 0.026 0.002 PHE D 378 TYR 0.010 0.001 TYR L 487 ARG 0.004 0.000 ARG L 588 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 671) hydrogen bonds : angle 5.52651 ( 1881) covalent geometry : bond 0.00309 (23039) covalent geometry : angle 0.56329 (31271) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6002 (mt-10) REVERT: A 457 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7171 (m) REVERT: D 648 MET cc_start: 0.7695 (tpp) cc_final: 0.7439 (tpp) REVERT: M 257 LYS cc_start: 0.6788 (tptt) cc_final: 0.6562 (mptt) REVERT: M 377 GLU cc_start: 0.7388 (pt0) cc_final: 0.7113 (mm-30) REVERT: M 419 MET cc_start: 0.6951 (mmp) cc_final: 0.6081 (mmt) REVERT: M 452 ARG cc_start: 0.6060 (ttt180) cc_final: 0.4983 (ttt-90) REVERT: M 492 MET cc_start: 0.5089 (tpp) cc_final: 0.4658 (tpp) REVERT: M 592 ASP cc_start: 0.7930 (t0) cc_final: 0.7567 (t0) REVERT: M 641 ILE cc_start: 0.7768 (tt) cc_final: 0.7440 (mt) REVERT: O 81 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8158 (pt0) REVERT: O 200 ILE cc_start: 0.8250 (mm) cc_final: 0.7974 (mm) REVERT: O 332 LEU cc_start: 0.8271 (tp) cc_final: 0.8037 (tp) REVERT: O 472 ILE cc_start: 0.8200 (mt) cc_final: 0.7953 (mm) REVERT: L 97 GLU cc_start: 0.6013 (tt0) cc_final: 0.5769 (tt0) REVERT: L 464 TYR cc_start: 0.8198 (m-80) cc_final: 0.7912 (m-80) REVERT: L 485 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7256 (pmt170) outliers start: 67 outliers final: 35 residues processed: 313 average time/residue: 0.3028 time to fit residues: 152.7115 Evaluate side-chains 277 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 530 VAL Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 220 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 218 optimal weight: 0.0040 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 212 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS M 508 GLN M 525 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN L 18 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150799 restraints weight = 38565.109| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.37 r_work: 0.3853 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23040 Z= 0.123 Angle : 0.549 8.974 31271 Z= 0.279 Chirality : 0.045 0.186 3621 Planarity : 0.004 0.055 3983 Dihedral : 7.284 123.693 3243 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.06 % Allowed : 14.14 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2896 helix: 0.03 (0.18), residues: 869 sheet: -1.13 (0.25), residues: 426 loop : -1.05 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 231 HIS 0.007 0.001 HIS L 162 PHE 0.025 0.001 PHE D 378 TYR 0.011 0.001 TYR A 130 ARG 0.005 0.000 ARG L 588 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 671) hydrogen bonds : angle 5.34567 ( 1881) covalent geometry : bond 0.00296 (23039) covalent geometry : angle 0.54869 (31271) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.7395 (mmp) cc_final: 0.6964 (ptt) REVERT: A 457 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7169 (m) REVERT: A 496 GLN cc_start: 0.7828 (mt0) cc_final: 0.7564 (mt0) REVERT: D 81 GLU cc_start: 0.7863 (pt0) cc_final: 0.7566 (mp0) REVERT: D 237 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6172 (mt-10) REVERT: D 648 MET cc_start: 0.7846 (tpp) cc_final: 0.7550 (tpp) REVERT: M 377 GLU cc_start: 0.7398 (pt0) cc_final: 0.7138 (mm-30) REVERT: M 404 TRP cc_start: 0.7542 (m-10) cc_final: 0.7116 (m-10) REVERT: M 419 MET cc_start: 0.7049 (mmt) cc_final: 0.6092 (mmt) REVERT: M 452 ARG cc_start: 0.5992 (ttt180) cc_final: 0.4968 (ttt-90) REVERT: M 492 MET cc_start: 0.5209 (tpp) cc_final: 0.4840 (tpp) REVERT: M 517 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6417 (ttt) REVERT: M 592 ASP cc_start: 0.7934 (t0) cc_final: 0.7578 (t0) REVERT: M 641 ILE cc_start: 0.7777 (tt) cc_final: 0.7499 (mt) REVERT: O 92 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7273 (m) REVERT: O 200 ILE cc_start: 0.8212 (mm) cc_final: 0.7975 (mm) REVERT: O 560 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.5908 (ptp) REVERT: L 332 LEU cc_start: 0.7674 (mt) cc_final: 0.7314 (mp) REVERT: L 419 MET cc_start: 0.7097 (mmm) cc_final: 0.6805 (mmt) REVERT: L 464 TYR cc_start: 0.8192 (m-80) cc_final: 0.7907 (m-80) REVERT: L 485 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7296 (pmt170) REVERT: L 564 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7723 (mp) outliers start: 74 outliers final: 46 residues processed: 314 average time/residue: 0.2955 time to fit residues: 150.0834 Evaluate side-chains 290 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 472 ILE Chi-restraints excluded: chain M residue 508 GLN Chi-restraints excluded: chain M residue 517 MET Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 564 ILE Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 104 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 129 optimal weight: 40.0000 chunk 160 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN M 119 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.176831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.143228 restraints weight = 38496.820| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.30 r_work: 0.3766 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 23040 Z= 0.267 Angle : 0.700 9.682 31271 Z= 0.361 Chirality : 0.050 0.165 3621 Planarity : 0.005 0.063 3983 Dihedral : 7.785 122.374 3243 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.18 % Allowed : 15.01 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.15), residues: 2896 helix: -0.45 (0.17), residues: 859 sheet: -1.31 (0.25), residues: 421 loop : -1.23 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 231 HIS 0.018 0.002 HIS L 162 PHE 0.043 0.003 PHE D 378 TYR 0.020 0.002 TYR A 130 ARG 0.005 0.001 ARG L 588 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 671) hydrogen bonds : angle 5.67504 ( 1881) covalent geometry : bond 0.00656 (23039) covalent geometry : angle 0.70050 (31271) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 248 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: A 457 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7134 (m) REVERT: D 81 GLU cc_start: 0.7965 (pt0) cc_final: 0.7568 (mp0) REVERT: D 88 ARG cc_start: 0.6981 (mmm160) cc_final: 0.6380 (mpt180) REVERT: D 237 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6384 (mt-10) REVERT: D 648 MET cc_start: 0.7918 (tpp) cc_final: 0.7635 (tpp) REVERT: M 377 GLU cc_start: 0.7750 (pt0) cc_final: 0.7403 (mm-30) REVERT: M 404 TRP cc_start: 0.7619 (m-10) cc_final: 0.7346 (m-10) REVERT: M 419 MET cc_start: 0.7306 (mmt) cc_final: 0.6498 (mmt) REVERT: M 452 ARG cc_start: 0.6000 (ttt180) cc_final: 0.2949 (tpm170) REVERT: M 492 MET cc_start: 0.5356 (tpp) cc_final: 0.4894 (tpp) REVERT: M 592 ASP cc_start: 0.8067 (t0) cc_final: 0.7739 (t0) REVERT: O 200 ILE cc_start: 0.8370 (mm) cc_final: 0.8093 (mm) REVERT: O 560 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6279 (ptp) REVERT: O 603 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7875 (mmtp) REVERT: O 677 GLU cc_start: 0.7103 (tm-30) cc_final: 0.5882 (mm-30) REVERT: L 419 MET cc_start: 0.7502 (mmm) cc_final: 0.7157 (mmt) REVERT: L 464 TYR cc_start: 0.8288 (m-80) cc_final: 0.7990 (m-80) REVERT: L 485 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7304 (pmt170) REVERT: L 574 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8067 (m-30) outliers start: 101 outliers final: 73 residues processed: 322 average time/residue: 0.3204 time to fit residues: 165.8494 Evaluate side-chains 314 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 526 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain O residue 603 LYS Chi-restraints excluded: chain O residue 662 TYR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 574 ASP Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain L residue 668 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 67 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 265 optimal weight: 0.3980 chunk 214 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN O 689 ASN L 18 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.149267 restraints weight = 38309.018| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.38 r_work: 0.3848 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23040 Z= 0.107 Angle : 0.557 11.300 31271 Z= 0.282 Chirality : 0.045 0.192 3621 Planarity : 0.004 0.049 3983 Dihedral : 7.288 123.716 3243 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.32 % Allowed : 17.61 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 2896 helix: -0.03 (0.18), residues: 866 sheet: -1.18 (0.25), residues: 424 loop : -1.05 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 231 HIS 0.009 0.001 HIS M 670 PHE 0.023 0.001 PHE O 294 TYR 0.014 0.001 TYR A 130 ARG 0.006 0.000 ARG L 516 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 671) hydrogen bonds : angle 5.32843 ( 1881) covalent geometry : bond 0.00248 (23039) covalent geometry : angle 0.55681 (31271) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.7356 (mmp) cc_final: 0.7034 (ptt) REVERT: A 457 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7191 (m) REVERT: A 496 GLN cc_start: 0.7805 (mt0) cc_final: 0.7486 (mt0) REVERT: D 81 GLU cc_start: 0.7991 (pt0) cc_final: 0.7622 (mp0) REVERT: D 237 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6252 (mt-10) REVERT: D 538 MET cc_start: 0.7868 (mmm) cc_final: 0.7564 (mmm) REVERT: D 648 MET cc_start: 0.7988 (tpp) cc_final: 0.7718 (tpp) REVERT: M 240 SER cc_start: 0.6268 (t) cc_final: 0.5728 (p) REVERT: M 377 GLU cc_start: 0.7658 (pt0) cc_final: 0.7350 (mm-30) REVERT: M 404 TRP cc_start: 0.7523 (m-10) cc_final: 0.7312 (m-10) REVERT: M 419 MET cc_start: 0.7197 (mmt) cc_final: 0.6327 (mmt) REVERT: M 452 ARG cc_start: 0.5847 (ttt180) cc_final: 0.2884 (tpm170) REVERT: M 492 MET cc_start: 0.5214 (tpp) cc_final: 0.4685 (tpp) REVERT: M 592 ASP cc_start: 0.8008 (t0) cc_final: 0.7666 (t0) REVERT: M 641 ILE cc_start: 0.7705 (tt) cc_final: 0.7372 (mt) REVERT: O 92 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7250 (m) REVERT: O 200 ILE cc_start: 0.8172 (mm) cc_final: 0.7912 (mm) REVERT: O 677 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6003 (mm-30) REVERT: L 332 LEU cc_start: 0.7553 (mt) cc_final: 0.7249 (mp) REVERT: L 419 MET cc_start: 0.7535 (mmm) cc_final: 0.7291 (mmt) REVERT: L 464 TYR cc_start: 0.8183 (m-80) cc_final: 0.7968 (m-80) REVERT: L 485 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7267 (pmt170) outliers start: 56 outliers final: 33 residues processed: 305 average time/residue: 0.3228 time to fit residues: 156.5367 Evaluate side-chains 275 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 39 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 282 optimal weight: 0.0000 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 HIS M 162 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 689 ASN L 18 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.175945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143165 restraints weight = 38865.934| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.13 r_work: 0.3755 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 23040 Z= 0.273 Angle : 0.702 9.787 31271 Z= 0.359 Chirality : 0.050 0.171 3621 Planarity : 0.005 0.063 3983 Dihedral : 7.829 121.881 3243 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.06 % Allowed : 17.65 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.15), residues: 2896 helix: -0.48 (0.17), residues: 866 sheet: -1.27 (0.25), residues: 432 loop : -1.22 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 231 HIS 0.017 0.002 HIS L 162 PHE 0.047 0.003 PHE D 378 TYR 0.022 0.002 TYR A 130 ARG 0.007 0.001 ARG M 601 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 671) hydrogen bonds : angle 5.64276 ( 1881) covalent geometry : bond 0.00670 (23039) covalent geometry : angle 0.70242 (31271) Misc. bond : bond 0.00150 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 244 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7124 (m) REVERT: D 81 GLU cc_start: 0.7977 (pt0) cc_final: 0.7578 (mp0) REVERT: D 88 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6480 (mpt180) REVERT: D 237 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6390 (mt-10) REVERT: D 538 MET cc_start: 0.8051 (mmm) cc_final: 0.7671 (mmm) REVERT: M 377 GLU cc_start: 0.7916 (pt0) cc_final: 0.7593 (mm-30) REVERT: M 404 TRP cc_start: 0.7613 (m-10) cc_final: 0.7411 (m-10) REVERT: M 419 MET cc_start: 0.7286 (mmt) cc_final: 0.6481 (mmt) REVERT: M 452 ARG cc_start: 0.5911 (ttt180) cc_final: 0.2974 (tpm170) REVERT: M 492 MET cc_start: 0.5423 (tpp) cc_final: 0.5010 (tpp) REVERT: M 592 ASP cc_start: 0.8202 (t0) cc_final: 0.7927 (t0) REVERT: O 200 ILE cc_start: 0.8315 (mm) cc_final: 0.8040 (mm) REVERT: O 560 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6365 (ptp) REVERT: L 18 GLN cc_start: 0.7572 (mm110) cc_final: 0.7319 (mm-40) REVERT: L 419 MET cc_start: 0.7400 (mmm) cc_final: 0.7152 (mmt) REVERT: L 464 TYR cc_start: 0.8350 (m-80) cc_final: 0.8070 (m-80) REVERT: L 485 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7328 (pmt170) outliers start: 74 outliers final: 62 residues processed: 298 average time/residue: 0.3180 time to fit residues: 150.6213 Evaluate side-chains 296 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 508 GLN Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 665 VAL Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain O residue 662 TYR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 648 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 104 optimal weight: 0.0020 chunk 251 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 233 optimal weight: 0.7980 chunk 184 optimal weight: 0.1980 chunk 268 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 HIS M 508 GLN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 689 ASN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.147355 restraints weight = 38399.287| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.36 r_work: 0.3825 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23040 Z= 0.111 Angle : 0.581 10.182 31271 Z= 0.292 Chirality : 0.046 0.181 3621 Planarity : 0.004 0.056 3983 Dihedral : 7.354 122.666 3243 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.40 % Allowed : 18.52 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2896 helix: -0.09 (0.18), residues: 870 sheet: -1.13 (0.25), residues: 433 loop : -1.07 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 231 HIS 0.010 0.001 HIS M 670 PHE 0.022 0.001 PHE D 378 TYR 0.014 0.001 TYR A 130 ARG 0.006 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 671) hydrogen bonds : angle 5.31859 ( 1881) covalent geometry : bond 0.00263 (23039) covalent geometry : angle 0.58080 (31271) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.7309 (mmp) cc_final: 0.6998 (ptt) REVERT: A 457 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7233 (m) REVERT: D 81 GLU cc_start: 0.7954 (pt0) cc_final: 0.7462 (mp0) REVERT: D 88 ARG cc_start: 0.7039 (mmm160) cc_final: 0.6428 (tpp-160) REVERT: D 237 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6236 (mt-10) REVERT: D 372 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8111 (ptpp) REVERT: D 408 GLU cc_start: 0.7604 (pm20) cc_final: 0.7401 (pm20) REVERT: D 538 MET cc_start: 0.7793 (mmm) cc_final: 0.7513 (mmm) REVERT: M 377 GLU cc_start: 0.7718 (pt0) cc_final: 0.7445 (mm-30) REVERT: M 419 MET cc_start: 0.7189 (mmt) cc_final: 0.6468 (mmt) REVERT: M 452 ARG cc_start: 0.5932 (ttt180) cc_final: 0.3013 (tpm170) REVERT: M 492 MET cc_start: 0.5406 (tpp) cc_final: 0.5145 (tpp) REVERT: M 592 ASP cc_start: 0.8053 (t0) cc_final: 0.7830 (t0) REVERT: M 641 ILE cc_start: 0.7738 (tt) cc_final: 0.7474 (mt) REVERT: O 92 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7228 (m) REVERT: O 200 ILE cc_start: 0.8118 (mm) cc_final: 0.7875 (mm) REVERT: O 538 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: O 677 GLU cc_start: 0.6826 (tm-30) cc_final: 0.5307 (mm-30) REVERT: L 332 LEU cc_start: 0.7469 (mt) cc_final: 0.7154 (mp) REVERT: L 485 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7163 (pmt170) outliers start: 58 outliers final: 43 residues processed: 292 average time/residue: 0.3156 time to fit residues: 147.0357 Evaluate side-chains 295 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 508 GLN Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 170 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 248 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.179296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145816 restraints weight = 37681.498| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.30 r_work: 0.3802 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23040 Z= 0.152 Angle : 0.595 9.629 31271 Z= 0.301 Chirality : 0.046 0.178 3621 Planarity : 0.004 0.052 3983 Dihedral : 7.403 122.286 3243 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.44 % Allowed : 18.73 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.15), residues: 2896 helix: -0.09 (0.18), residues: 878 sheet: -1.15 (0.25), residues: 428 loop : -1.08 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 231 HIS 0.011 0.001 HIS M 670 PHE 0.030 0.002 PHE D 378 TYR 0.014 0.001 TYR D 60 ARG 0.006 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 671) hydrogen bonds : angle 5.29145 ( 1881) covalent geometry : bond 0.00374 (23039) covalent geometry : angle 0.59469 (31271) Misc. bond : bond 0.00084 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7226 (m) REVERT: D 81 GLU cc_start: 0.7934 (pt0) cc_final: 0.7483 (mp0) REVERT: D 88 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6375 (mpt180) REVERT: D 237 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6294 (mt-10) REVERT: D 372 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8138 (ptpp) REVERT: D 408 GLU cc_start: 0.7714 (pm20) cc_final: 0.7489 (pm20) REVERT: D 538 MET cc_start: 0.7854 (mmm) cc_final: 0.7567 (mmm) REVERT: M 377 GLU cc_start: 0.7776 (pt0) cc_final: 0.7484 (mm-30) REVERT: M 419 MET cc_start: 0.7216 (mmt) cc_final: 0.6410 (mmt) REVERT: M 452 ARG cc_start: 0.5859 (ttt180) cc_final: 0.2966 (tpm170) REVERT: M 492 MET cc_start: 0.5511 (tpp) cc_final: 0.5174 (tpp) REVERT: M 592 ASP cc_start: 0.8100 (t0) cc_final: 0.7896 (t0) REVERT: M 641 ILE cc_start: 0.7736 (tt) cc_final: 0.7462 (mt) REVERT: O 89 TRP cc_start: 0.5574 (m100) cc_final: 0.5277 (m100) REVERT: O 200 ILE cc_start: 0.8214 (mm) cc_final: 0.7968 (mm) REVERT: O 538 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7560 (mtm) REVERT: O 560 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6489 (ptp) REVERT: O 677 GLU cc_start: 0.6892 (tm-30) cc_final: 0.5434 (mm-30) REVERT: L 332 LEU cc_start: 0.7419 (mt) cc_final: 0.7101 (mp) REVERT: L 419 MET cc_start: 0.6990 (mmt) cc_final: 0.6433 (mmt) REVERT: L 485 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7211 (pmt170) REVERT: L 687 ILE cc_start: 0.7670 (mm) cc_final: 0.7444 (mm) outliers start: 59 outliers final: 44 residues processed: 293 average time/residue: 0.3280 time to fit residues: 153.7600 Evaluate side-chains 292 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 508 GLN Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 533 SER Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 191 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 193 optimal weight: 40.0000 chunk 203 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 237 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 162 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 = 0.4382 r_free = 0.4382 target = 0.181686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148119 restraints weight = 38176.789| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.46 r_work: 0.3828 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23040 Z= 0.114 Angle : 0.564 9.638 31271 Z= 0.284 Chirality : 0.045 0.182 3621 Planarity : 0.004 0.053 3983 Dihedral : 7.204 122.291 3243 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.23 % Allowed : 18.81 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2896 helix: 0.07 (0.18), residues: 880 sheet: -1.08 (0.25), residues: 422 loop : -0.97 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 231 HIS 0.011 0.001 HIS M 670 PHE 0.022 0.001 PHE D 378 TYR 0.013 0.001 TYR D 204 ARG 0.007 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 671) hydrogen bonds : angle 5.16452 ( 1881) covalent geometry : bond 0.00276 (23039) covalent geometry : angle 0.56426 (31271) Misc. bond : bond 0.00041 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10188.83 seconds wall clock time: 177 minutes 11.12 seconds (10631.12 seconds total)