Starting phenix.real_space_refine on Sun Aug 24 20:02:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wiv_37569/08_2025/8wiv_37569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wiv_37569/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wiv_37569/08_2025/8wiv_37569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wiv_37569/08_2025/8wiv_37569.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wiv_37569/08_2025/8wiv_37569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wiv_37569/08_2025/8wiv_37569.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLU:plan': 3} 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: {'ASP:plan': 1, 'GLU:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 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: {'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'GLU:plan': 9, 'TYR:plan': 6, 'HIS:plan': 5, 'GLN:plan1': 3, 'PHE: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: {'PHE:plan': 1, 'TYR:plan': 7, 'ARG:plan': 3, 'HIS:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 2} 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: {'ASP:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 3} 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: 4.54, per 1000 atoms: 0.20 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: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 3.42 Time building geometry restraints manager: 2.10 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: 1.040 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.090 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG L 161 TYR 0.033 0.001 TYR O 662 PHE 0.023 0.002 PHE O 534 TRP 0.050 0.002 TRP D 441 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00756 (23039) covalent geometry : angle 0.64609 (31271) hydrogen bonds : bond 0.26654 ( 671) hydrogen bonds : angle 9.34894 ( 1881) 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 : 0.865 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: 0.7482 (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: 0.7315 (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: 0.1366 time to fit residues: 81.0762 Evaluate side-chains 258 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 L 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.181340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148154 restraints weight = 38224.590| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.17 r_work: 0.3819 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23040 Z= 0.199 Angle : 0.674 9.918 31271 Z= 0.349 Chirality : 0.050 0.202 3621 Planarity : 0.005 0.059 3983 Dihedral : 7.486 124.033 3243 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.61 % Allowed : 8.81 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.15), residues: 2896 helix: -0.49 (0.17), residues: 858 sheet: -1.60 (0.25), residues: 422 loop : -1.20 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 55 TYR 0.023 0.002 TYR O 662 PHE 0.020 0.002 PHE A 243 TRP 0.022 0.002 TRP D 441 HIS 0.012 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00478 (23039) covalent geometry : angle 0.67442 (31271) hydrogen bonds : bond 0.05704 ( 671) hydrogen bonds : angle 6.30832 ( 1881) Misc. bond : bond 0.00149 ( 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 321 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.5753 (ttpp) cc_final: 0.4543 (tptt) REVERT: A 457 VAL cc_start: 0.7513 (p) cc_final: 0.7152 (m) REVERT: D 247 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6816 (mm-30) REVERT: M 377 GLU cc_start: 0.7284 (pt0) cc_final: 0.7017 (mm-30) REVERT: M 492 MET cc_start: 0.5447 (tpp) cc_final: 0.4860 (tpp) REVERT: O 332 LEU cc_start: 0.8634 (tp) cc_final: 0.8428 (tp) REVERT: O 500 GLU cc_start: 0.7865 (tp30) cc_final: 0.7602 (tp30) REVERT: L 437 ASP cc_start: 0.7656 (m-30) cc_final: 0.7442 (m-30) REVERT: L 464 TYR cc_start: 0.8387 (m-80) cc_final: 0.7993 (m-80) REVERT: L 532 ASP cc_start: 0.6975 (t0) cc_final: 0.6729 (t0) REVERT: L 538 MET cc_start: 0.7100 (mmm) cc_final: 0.6832 (mmm) outliers start: 39 outliers final: 24 residues processed: 306 average time/residue: 0.1347 time to fit residues: 66.0493 Evaluate side-chains 265 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 432 ILE 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 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 434 ILE 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 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 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 263 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** O 689 ASN L 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.149533 restraints weight = 38424.442| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.42 r_work: 0.3838 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23040 Z= 0.145 Angle : 0.597 10.151 31271 Z= 0.304 Chirality : 0.047 0.192 3621 Planarity : 0.004 0.052 3983 Dihedral : 7.437 123.305 3243 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.19 % Allowed : 12.07 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.15), residues: 2896 helix: -0.32 (0.18), residues: 869 sheet: -1.38 (0.25), residues: 419 loop : -1.12 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 545 TYR 0.015 0.001 TYR A 130 PHE 0.023 0.002 PHE D 378 TRP 0.016 0.001 TRP L 404 HIS 0.008 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00350 (23039) covalent geometry : angle 0.59713 (31271) hydrogen bonds : bond 0.04532 ( 671) hydrogen bonds : angle 5.81328 ( 1881) Misc. bond : bond 0.00001 ( 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 329 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7159 (m) REVERT: D 81 GLU cc_start: 0.7891 (pt0) cc_final: 0.7624 (mp0) REVERT: M 377 GLU cc_start: 0.7382 (pt0) cc_final: 0.7150 (mm-30) REVERT: M 492 MET cc_start: 0.5189 (tpp) cc_final: 0.4683 (tpp) REVERT: M 532 ASP cc_start: 0.6054 (t0) cc_final: 0.5786 (p0) REVERT: M 592 ASP cc_start: 0.7881 (t0) cc_final: 0.7414 (t0) REVERT: M 641 ILE cc_start: 0.7724 (tt) cc_final: 0.7317 (mt) REVERT: O 200 ILE cc_start: 0.8294 (mm) cc_final: 0.7969 (mm) REVERT: O 332 LEU cc_start: 0.8531 (tp) cc_final: 0.8279 (tp) REVERT: O 472 ILE cc_start: 0.8343 (mt) cc_final: 0.8114 (mm) REVERT: O 560 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5863 (ptp) REVERT: L 268 ARG cc_start: 0.7229 (ptp-170) cc_final: 0.6575 (ptp-170) REVERT: L 419 MET cc_start: 0.7791 (mmp) cc_final: 0.6981 (mmt) REVERT: L 464 TYR cc_start: 0.8278 (m-80) cc_final: 0.7989 (m-80) REVERT: L 532 ASP cc_start: 0.7022 (t0) cc_final: 0.6767 (t0) REVERT: L 592 ASP cc_start: 0.7534 (t0) cc_final: 0.7326 (t0) outliers start: 53 outliers final: 32 residues processed: 310 average time/residue: 0.1332 time to fit residues: 66.2642 Evaluate side-chains 279 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE 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 457 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 138 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 260 optimal weight: 40.0000 chunk 143 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 230 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS M 525 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.149665 restraints weight = 38542.183| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.50 r_work: 0.3832 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2333 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= 0.136 Angle : 0.573 9.809 31271 Z= 0.292 Chirality : 0.046 0.201 3621 Planarity : 0.004 0.049 3983 Dihedral : 7.379 123.505 3243 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.94 % Allowed : 13.31 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 2896 helix: -0.14 (0.18), residues: 867 sheet: -1.29 (0.25), residues: 422 loop : -1.06 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 588 TYR 0.011 0.001 TYR D 60 PHE 0.028 0.002 PHE O 294 TRP 0.013 0.001 TRP D 231 HIS 0.009 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00328 (23039) covalent geometry : angle 0.57290 (31271) hydrogen bonds : bond 0.03957 ( 671) hydrogen bonds : angle 5.52150 ( 1881) Misc. bond : bond 0.00020 ( 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 336 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 265 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.7231 (mmp) cc_final: 0.6934 (ptt) REVERT: A 457 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7191 (m) REVERT: D 81 GLU cc_start: 0.7947 (pt0) cc_final: 0.7451 (mp0) REVERT: D 560 MET cc_start: 0.6021 (mmt) cc_final: 0.5684 (mmt) REVERT: D 648 MET cc_start: 0.7741 (tpp) cc_final: 0.7468 (tpp) REVERT: M 257 LYS cc_start: 0.6793 (tptt) cc_final: 0.6568 (mptt) REVERT: M 377 GLU cc_start: 0.7361 (pt0) cc_final: 0.7122 (mm-30) REVERT: M 419 MET cc_start: 0.6974 (mmp) cc_final: 0.6239 (mmt) REVERT: M 452 ARG cc_start: 0.6075 (ttt180) cc_final: 0.5029 (ttt-90) REVERT: M 492 MET cc_start: 0.5206 (tpp) cc_final: 0.4769 (tpp) REVERT: M 592 ASP cc_start: 0.7952 (t0) cc_final: 0.7591 (t0) REVERT: M 641 ILE cc_start: 0.7781 (tt) cc_final: 0.7434 (mt) REVERT: O 92 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7333 (m) REVERT: O 200 ILE cc_start: 0.8237 (mm) cc_final: 0.7947 (mm) REVERT: O 332 LEU cc_start: 0.8328 (tp) cc_final: 0.8067 (tp) REVERT: O 472 ILE cc_start: 0.8219 (mt) cc_final: 0.7979 (mm) REVERT: O 560 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.5837 (ptp) REVERT: L 97 GLU cc_start: 0.6053 (tt0) cc_final: 0.5786 (tt0) REVERT: L 419 MET cc_start: 0.7732 (mmp) cc_final: 0.6966 (mmt) REVERT: L 464 TYR cc_start: 0.8266 (m-80) cc_final: 0.7970 (m-80) REVERT: L 485 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7499 (pmt170) outliers start: 71 outliers final: 39 residues processed: 315 average time/residue: 0.1321 time to fit residues: 67.6796 Evaluate side-chains 289 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 132 THR Chi-restraints excluded: chain D residue 546 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 138 ILE 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 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 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 281 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 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 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 225 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 M 508 GLN ** 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 670 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.178390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.145547 restraints weight = 38600.834| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.17 r_work: 0.3780 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23040 Z= 0.227 Angle : 0.656 10.287 31271 Z= 0.336 Chirality : 0.048 0.207 3621 Planarity : 0.005 0.060 3983 Dihedral : 7.654 122.731 3243 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.68 % Allowed : 14.59 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.15), residues: 2896 helix: -0.34 (0.18), residues: 852 sheet: -1.35 (0.25), residues: 424 loop : -1.22 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 588 TYR 0.017 0.002 TYR A 130 PHE 0.037 0.002 PHE D 378 TRP 0.021 0.002 TRP O 231 HIS 0.015 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00560 (23039) covalent geometry : angle 0.65636 (31271) hydrogen bonds : bond 0.04523 ( 671) hydrogen bonds : angle 5.62989 ( 1881) Misc. bond : bond 0.00048 ( 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 341 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 252 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7115 (m) REVERT: D 81 GLU cc_start: 0.8033 (pt0) cc_final: 0.7434 (mp0) REVERT: D 237 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6257 (mt-10) REVERT: D 648 MET cc_start: 0.7886 (tpp) cc_final: 0.7519 (tpp) REVERT: M 377 GLU cc_start: 0.7564 (pt0) cc_final: 0.7281 (mm-30) REVERT: M 419 MET cc_start: 0.7230 (mmp) cc_final: 0.6451 (mmt) REVERT: M 452 ARG cc_start: 0.5938 (ttt180) cc_final: 0.4747 (ttt-90) REVERT: M 492 MET cc_start: 0.5320 (tpp) cc_final: 0.4881 (tpp) REVERT: M 592 ASP cc_start: 0.8092 (t0) cc_final: 0.7711 (t0) REVERT: O 117 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7217 (mtpt) REVERT: O 200 ILE cc_start: 0.8381 (mm) cc_final: 0.8093 (mm) REVERT: O 332 LEU cc_start: 0.8449 (tp) cc_final: 0.8245 (tp) REVERT: O 560 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6253 (ptp) REVERT: L 186 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (t0) REVERT: L 419 MET cc_start: 0.7776 (mmp) cc_final: 0.7001 (mmt) REVERT: L 464 TYR cc_start: 0.8321 (m-80) cc_final: 0.8015 (m-80) REVERT: L 485 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7356 (pmt170) REVERT: L 538 MET cc_start: 0.7221 (mmm) cc_final: 0.6971 (mmm) outliers start: 89 outliers final: 65 residues processed: 311 average time/residue: 0.1286 time to fit residues: 64.7775 Evaluate side-chains 303 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 184 ILE 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 401 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 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 432 ILE 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 576 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 138 ILE 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 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 517 MET Chi-restraints excluded: chain M residue 532 ASP 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 178 THR Chi-restraints excluded: chain O residue 214 VAL 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 401 LEU Chi-restraints excluded: chain O residue 530 VAL 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 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 186 ASP Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 297 TYR 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 665 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 96 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 215 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.182656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.149329 restraints weight = 38369.396| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.37 r_work: 0.3847 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23040 Z= 0.109 Angle : 0.550 8.995 31271 Z= 0.281 Chirality : 0.046 0.189 3621 Planarity : 0.004 0.050 3983 Dihedral : 7.306 123.694 3243 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.65 % Allowed : 16.58 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.15), residues: 2896 helix: -0.09 (0.18), residues: 865 sheet: -1.18 (0.25), residues: 424 loop : -1.05 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 516 TYR 0.012 0.001 TYR A 130 PHE 0.022 0.001 PHE D 378 TRP 0.014 0.001 TRP D 231 HIS 0.009 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00257 (23039) covalent geometry : angle 0.54972 (31271) hydrogen bonds : bond 0.03506 ( 671) hydrogen bonds : angle 5.36841 ( 1881) Misc. bond : bond 0.00034 ( 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 333 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.7259 (mmp) cc_final: 0.6988 (ptt) REVERT: A 457 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7264 (m) REVERT: D 81 GLU cc_start: 0.8026 (pt0) cc_final: 0.7481 (mp0) REVERT: D 237 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6151 (mt-10) REVERT: D 560 MET cc_start: 0.6061 (mmt) cc_final: 0.5654 (mmt) REVERT: D 648 MET cc_start: 0.7853 (tpp) cc_final: 0.7557 (tpp) REVERT: M 419 MET cc_start: 0.7179 (mmt) cc_final: 0.6311 (mmt) REVERT: M 452 ARG cc_start: 0.5916 (ttt180) cc_final: 0.4878 (ttt-90) REVERT: M 492 MET cc_start: 0.5244 (tpp) cc_final: 0.4894 (tpp) REVERT: M 592 ASP cc_start: 0.7961 (t0) cc_final: 0.7609 (t0) REVERT: M 641 ILE cc_start: 0.7732 (tt) cc_final: 0.7388 (mt) REVERT: O 92 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7231 (m) REVERT: O 200 ILE cc_start: 0.8193 (mm) cc_final: 0.7932 (mm) REVERT: O 560 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6017 (ptp) REVERT: L 186 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7822 (t0) REVERT: L 332 LEU cc_start: 0.7673 (mt) cc_final: 0.7275 (mp) REVERT: L 419 MET cc_start: 0.7659 (mmp) cc_final: 0.6953 (mmt) REVERT: L 464 TYR cc_start: 0.8171 (m-80) cc_final: 0.7951 (m-80) REVERT: L 485 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7227 (pmt170) outliers start: 64 outliers final: 40 residues processed: 314 average time/residue: 0.1316 time to fit residues: 66.0458 Evaluate side-chains 288 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 252 ASN 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 538 MET 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 480 ILE Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 552 ILE 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 126 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 158 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 508 GLN Chi-restraints excluded: chain M residue 532 ASP 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 179 SER 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 94 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 281 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.178065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144687 restraints weight = 38456.404| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.10 r_work: 0.3781 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23040 Z= 0.208 Angle : 0.633 8.403 31271 Z= 0.323 Chirality : 0.048 0.177 3621 Planarity : 0.005 0.061 3983 Dihedral : 7.596 122.489 3243 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.68 % Allowed : 16.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 2896 helix: -0.31 (0.17), residues: 872 sheet: -1.25 (0.25), residues: 424 loop : -1.15 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 516 TYR 0.017 0.002 TYR A 130 PHE 0.037 0.002 PHE D 378 TRP 0.021 0.002 TRP O 231 HIS 0.015 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00515 (23039) covalent geometry : angle 0.63304 (31271) hydrogen bonds : bond 0.04241 ( 671) hydrogen bonds : angle 5.49340 ( 1881) Misc. bond : bond 0.00125 ( 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 339 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 250 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.6378 (ttpp) cc_final: 0.5203 (tppt) REVERT: A 419 MET cc_start: 0.7284 (mmp) cc_final: 0.7072 (ptt) REVERT: A 457 VAL cc_start: 0.7582 (OUTLIER) cc_final: 0.7177 (m) REVERT: D 81 GLU cc_start: 0.8020 (pt0) cc_final: 0.7446 (mp0) REVERT: D 88 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6368 (mpt180) REVERT: D 237 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6288 (mt-10) REVERT: D 560 MET cc_start: 0.6105 (mmt) cc_final: 0.5702 (mmt) REVERT: D 648 MET cc_start: 0.7959 (tpp) cc_final: 0.7679 (tpp) REVERT: M 419 MET cc_start: 0.7279 (mmt) cc_final: 0.6456 (mmt) REVERT: M 452 ARG cc_start: 0.5889 (ttt180) cc_final: 0.2969 (tpm170) REVERT: M 492 MET cc_start: 0.5321 (tpp) cc_final: 0.4910 (tpp) REVERT: M 592 ASP cc_start: 0.8123 (t0) cc_final: 0.7780 (t0) REVERT: O 200 ILE cc_start: 0.8325 (mm) cc_final: 0.8059 (mm) REVERT: O 560 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6014 (ptp) REVERT: L 18 GLN cc_start: 0.7556 (mm110) cc_final: 0.7290 (mm-40) REVERT: L 186 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7961 (t0) REVERT: L 419 MET cc_start: 0.7758 (mmp) cc_final: 0.6873 (mmt) REVERT: L 485 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7292 (pmt170) REVERT: L 538 MET cc_start: 0.7282 (mmm) cc_final: 0.6904 (mmm) outliers start: 89 outliers final: 64 residues processed: 312 average time/residue: 0.1309 time to fit residues: 66.2947 Evaluate side-chains 302 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 VAL 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 457 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE 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 658 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 200 ILE 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 517 MET Chi-restraints excluded: chain M residue 526 VAL Chi-restraints excluded: chain M residue 532 ASP 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 178 THR Chi-restraints excluded: chain O residue 184 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 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 138 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 235 CYS 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 491 MET 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 648 MET Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain L residue 668 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 24 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 288 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.7484 ------------------------------------------------------------------------------- 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** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.179925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.146237 restraints weight = 38364.610| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.29 r_work: 0.3809 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3098 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= 0.136 Angle : 0.578 11.071 31271 Z= 0.293 Chirality : 0.046 0.262 3621 Planarity : 0.004 0.055 3983 Dihedral : 7.414 123.063 3243 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.81 % Allowed : 17.98 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 2896 helix: -0.13 (0.18), residues: 869 sheet: -1.08 (0.25), residues: 433 loop : -1.08 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 516 TYR 0.016 0.001 TYR A 130 PHE 0.031 0.002 PHE D 378 TRP 0.023 0.002 TRP M 404 HIS 0.009 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00333 (23039) covalent geometry : angle 0.57839 (31271) hydrogen bonds : bond 0.03638 ( 671) hydrogen bonds : angle 5.34062 ( 1881) Misc. bond : bond 0.00061 ( 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 319 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7150 (m) REVERT: D 81 GLU cc_start: 0.8044 (pt0) cc_final: 0.7509 (mp0) REVERT: D 237 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6256 (mt-10) REVERT: D 538 MET cc_start: 0.7837 (mmm) cc_final: 0.7528 (mmm) REVERT: D 560 MET cc_start: 0.6253 (mmt) cc_final: 0.5796 (mmt) REVERT: D 648 MET cc_start: 0.7998 (tpp) cc_final: 0.7735 (tpp) REVERT: M 419 MET cc_start: 0.7211 (mmt) cc_final: 0.6391 (mmt) REVERT: M 452 ARG cc_start: 0.5914 (ttt180) cc_final: 0.2960 (tpm170) REVERT: M 492 MET cc_start: 0.5432 (tpp) cc_final: 0.5074 (tpp) REVERT: M 592 ASP cc_start: 0.8038 (t0) cc_final: 0.7724 (t0) REVERT: M 641 ILE cc_start: 0.7706 (tt) cc_final: 0.7406 (mt) REVERT: O 92 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7226 (m) REVERT: O 200 ILE cc_start: 0.8205 (mm) cc_final: 0.7914 (mm) REVERT: O 560 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6064 (ptp) REVERT: L 332 LEU cc_start: 0.7593 (mt) cc_final: 0.7250 (mp) REVERT: L 419 MET cc_start: 0.7681 (mmp) cc_final: 0.6840 (mmt) REVERT: L 464 TYR cc_start: 0.8271 (m-80) cc_final: 0.7936 (m-80) REVERT: L 485 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7224 (pmt170) REVERT: L 538 MET cc_start: 0.7285 (mmm) cc_final: 0.6883 (mmm) outliers start: 68 outliers final: 55 residues processed: 295 average time/residue: 0.1292 time to fit residues: 61.1590 Evaluate side-chains 294 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain A residue 95 VAL 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 457 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE 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 658 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 217 VAL 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 517 MET Chi-restraints excluded: chain M residue 532 ASP 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 184 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 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 235 CYS Chi-restraints excluded: chain L residue 297 TYR 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 491 MET 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 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 62 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** M 119 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147644 restraints weight = 38162.462| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.46 r_work: 0.3823 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23040 Z= 0.119 Angle : 0.563 10.198 31271 Z= 0.283 Chirality : 0.046 0.251 3621 Planarity : 0.004 0.053 3983 Dihedral : 7.263 122.845 3243 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.44 % Allowed : 18.52 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.15), residues: 2896 helix: 0.00 (0.18), residues: 873 sheet: -1.04 (0.25), residues: 428 loop : -1.00 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.015 0.001 TYR A 130 PHE 0.022 0.001 PHE D 378 TRP 0.019 0.001 TRP L 404 HIS 0.010 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00288 (23039) covalent geometry : angle 0.56336 (31271) hydrogen bonds : bond 0.03375 ( 671) hydrogen bonds : angle 5.19837 ( 1881) Misc. bond : bond 0.00041 ( 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 306 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7254 (m) REVERT: A 496 GLN cc_start: 0.7942 (mt0) cc_final: 0.7646 (mt0) REVERT: D 81 GLU cc_start: 0.8034 (pt0) cc_final: 0.7505 (mp0) REVERT: D 88 ARG cc_start: 0.7030 (mmm160) cc_final: 0.6410 (tpp-160) REVERT: D 237 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6351 (mt-10) REVERT: D 538 MET cc_start: 0.7736 (mmm) cc_final: 0.7448 (mmm) REVERT: D 560 MET cc_start: 0.6132 (mmt) cc_final: 0.5675 (mmt) REVERT: M 419 MET cc_start: 0.7190 (mmt) cc_final: 0.6550 (mmt) REVERT: M 452 ARG cc_start: 0.5949 (ttt180) cc_final: 0.3041 (tpm170) REVERT: M 492 MET cc_start: 0.5506 (tpp) cc_final: 0.4999 (tpp) REVERT: M 592 ASP cc_start: 0.8052 (t0) cc_final: 0.7798 (t0) REVERT: M 641 ILE cc_start: 0.7750 (tt) cc_final: 0.7495 (mt) REVERT: O 89 TRP cc_start: 0.5510 (m100) cc_final: 0.5272 (m100) REVERT: O 92 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7333 (m) REVERT: O 200 ILE cc_start: 0.8143 (mm) cc_final: 0.7876 (mm) REVERT: O 560 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6118 (ptp) REVERT: L 332 LEU cc_start: 0.7474 (mt) cc_final: 0.7185 (mp) REVERT: L 419 MET cc_start: 0.7711 (mmp) cc_final: 0.7190 (mmt) REVERT: L 464 TYR cc_start: 0.8228 (m-80) cc_final: 0.7951 (m-80) REVERT: L 485 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7173 (pmt170) REVERT: L 538 MET cc_start: 0.7232 (mmm) cc_final: 0.6758 (mmm) outliers start: 59 outliers final: 44 residues processed: 282 average time/residue: 0.1289 time to fit residues: 58.6955 Evaluate side-chains 291 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 432 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 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 285 ILE 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 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 214 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 401 LEU 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 297 TYR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 491 MET 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 648 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 178 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 278 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.9244 ------------------------------------------------------------------------------- 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** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS M 162 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.180074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146271 restraints weight = 38388.671| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.25 r_work: 0.3819 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3346 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= 0.142 Angle : 0.579 9.936 31271 Z= 0.292 Chirality : 0.046 0.256 3621 Planarity : 0.004 0.052 3983 Dihedral : 7.300 122.540 3243 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.48 % Allowed : 18.73 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 2896 helix: 0.01 (0.18), residues: 874 sheet: -1.04 (0.25), residues: 428 loop : -1.02 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 588 TYR 0.016 0.001 TYR A 130 PHE 0.029 0.002 PHE D 378 TRP 0.019 0.002 TRP L 404 HIS 0.010 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00349 (23039) covalent geometry : angle 0.57929 (31271) hydrogen bonds : bond 0.03578 ( 671) hydrogen bonds : angle 5.20517 ( 1881) Misc. bond : bond 0.00085 ( 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 308 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7248 (m) REVERT: A 496 GLN cc_start: 0.7974 (mt0) cc_final: 0.7672 (mt0) REVERT: D 81 GLU cc_start: 0.8032 (pt0) cc_final: 0.7514 (mp0) REVERT: D 88 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6387 (tpp-160) REVERT: D 237 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6261 (mt-10) REVERT: D 538 MET cc_start: 0.7810 (mmm) cc_final: 0.7519 (mmm) REVERT: D 560 MET cc_start: 0.6163 (mmt) cc_final: 0.5681 (mmt) REVERT: M 419 MET cc_start: 0.7146 (mmt) cc_final: 0.6479 (mmt) REVERT: M 452 ARG cc_start: 0.5857 (ttt180) cc_final: 0.2975 (tpm170) REVERT: M 492 MET cc_start: 0.5498 (tpp) cc_final: 0.4985 (tpp) REVERT: M 592 ASP cc_start: 0.8078 (t0) cc_final: 0.7875 (t0) REVERT: M 641 ILE cc_start: 0.7729 (tt) cc_final: 0.7474 (mt) REVERT: O 92 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7274 (m) REVERT: O 200 ILE cc_start: 0.8264 (mm) cc_final: 0.7999 (mm) REVERT: O 560 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6161 (ptp) REVERT: O 677 GLU cc_start: 0.7140 (tm-30) cc_final: 0.5718 (mm-30) REVERT: L 332 LEU cc_start: 0.7475 (mt) cc_final: 0.7181 (mp) REVERT: L 419 MET cc_start: 0.7755 (mmp) cc_final: 0.6897 (mmt) REVERT: L 464 TYR cc_start: 0.8301 (m-80) cc_final: 0.7930 (m-80) REVERT: L 485 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7228 (pmt170) REVERT: L 538 MET cc_start: 0.7333 (mmm) cc_final: 0.6823 (mmm) REVERT: L 687 ILE cc_start: 0.7634 (mm) cc_final: 0.7413 (mm) outliers start: 60 outliers final: 50 residues processed: 286 average time/residue: 0.1310 time to fit residues: 60.4406 Evaluate side-chains 294 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 201 HIS Chi-restraints excluded: chain A residue 234 THR 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 504 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 438 SER 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 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 285 ILE 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 517 MET Chi-restraints excluded: chain M residue 532 ASP 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 292 LEU Chi-restraints excluded: chain O residue 401 LEU 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 235 CYS Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 491 MET 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 648 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 282 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 18 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- 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** M 119 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 689 ASN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.183290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.152531 restraints weight = 38357.990| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.96 r_work: 0.3889 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23040 Z= 0.152 Angle : 0.590 9.406 31271 Z= 0.298 Chirality : 0.047 0.260 3621 Planarity : 0.004 0.053 3983 Dihedral : 7.328 122.118 3243 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.60 % Allowed : 18.73 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.15), residues: 2896 helix: 0.01 (0.18), residues: 873 sheet: -1.11 (0.25), residues: 439 loop : -1.00 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 588 TYR 0.017 0.001 TYR A 130 PHE 0.030 0.002 PHE D 378 TRP 0.019 0.002 TRP L 404 HIS 0.010 0.001 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00375 (23039) covalent geometry : angle 0.58960 (31271) hydrogen bonds : bond 0.03646 ( 671) hydrogen bonds : angle 5.21411 ( 1881) Misc. bond : bond 0.00084 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.62 seconds wall clock time: 74 minutes 29.18 seconds (4469.18 seconds total)