Starting phenix.real_space_refine on Sun Sep 29 13:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wiv_37569/09_2024/8wiv_37569.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 14366 2.51 5 N 3867 2.21 5 O 4315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22622 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3133 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 5 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4667 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 26, 'TRANS': 575} Chain breaks: 4 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4757 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 29, 'TRANS': 600} Chain breaks: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 163 Chain: "O" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5002 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "L" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4935 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 30, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.86, per 1000 atoms: 0.61 Number of scatterers: 22622 At special positions: 0 Unit cell: (118.336, 137.7, 151.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 4 11.99 O 4315 8.00 N 3867 7.00 C 14366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.6 seconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 17 sheets defined 34.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 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: 6.96 Time building geometry restraints manager: 6.41 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 48.920 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.820 ------------------------------------------------------------------------------- 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 0.257 23039 Z= 0.496 Angle : 0.646 13.043 31271 Z= 0.428 Chirality : 0.045 0.238 3621 Planarity : 0.005 0.063 3983 Dihedral : 12.550 118.885 8457 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2896 helix: -0.73 (0.18), residues: 799 sheet: -1.85 (0.24), residues: 442 loop : -1.26 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 441 HIS 0.005 0.001 HIS A 162 PHE 0.023 0.002 PHE O 534 TYR 0.033 0.001 TYR O 662 ARG 0.007 0.001 ARG L 161 *********************** 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 fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7728 (p) cc_final: 0.7505 (m) REVERT: M 641 ILE cc_start: 0.7292 (tt) cc_final: 0.6632 (mt) REVERT: O 500 GLU cc_start: 0.7603 (tp30) cc_final: 0.7316 (tp30) REVERT: O 538 MET cc_start: 0.7496 (mmm) cc_final: 0.6982 (mmt) REVERT: O 540 MET cc_start: 0.6447 (ptp) cc_final: 0.6115 (ptp) REVERT: O 651 GLU cc_start: 0.7097 (pt0) cc_final: 0.6772 (pt0) REVERT: L 560 MET cc_start: 0.7323 (ptm) cc_final: 0.6684 (ptp) REVERT: L 686 GLN cc_start: 0.8010 (mt0) cc_final: 0.7417 (mt0) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.3342 time to fit residues: 195.4253 Evaluate side-chains 257 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 88 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 670 HIS L 119 HIS L 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23039 Z= 0.219 Angle : 0.629 8.946 31271 Z= 0.325 Chirality : 0.048 0.204 3621 Planarity : 0.004 0.046 3983 Dihedral : 7.280 125.434 3243 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.16 % Allowed : 8.56 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2896 helix: -0.33 (0.17), residues: 870 sheet: -1.51 (0.25), residues: 428 loop : -1.07 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 404 HIS 0.014 0.001 HIS A 162 PHE 0.019 0.002 PHE A 243 TYR 0.021 0.001 TYR O 662 ARG 0.006 0.001 ARG M 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 304 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.5624 (ttpp) cc_final: 0.4609 (tptt) REVERT: A 457 VAL cc_start: 0.7453 (p) cc_final: 0.7192 (m) REVERT: D 247 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6538 (mm-30) REVERT: M 492 MET cc_start: 0.5481 (tpp) cc_final: 0.4906 (tpp) REVERT: M 641 ILE cc_start: 0.7710 (tt) cc_final: 0.7344 (mt) REVERT: O 332 LEU cc_start: 0.8442 (tp) cc_final: 0.8238 (tp) REVERT: L 332 LEU cc_start: 0.7810 (mt) cc_final: 0.7419 (mp) REVERT: L 464 TYR cc_start: 0.8118 (m-80) cc_final: 0.7831 (m-80) REVERT: L 532 ASP cc_start: 0.6458 (t0) cc_final: 0.6163 (t0) outliers start: 28 outliers final: 15 residues processed: 322 average time/residue: 0.3216 time to fit residues: 163.8712 Evaluate side-chains 260 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 chunk 287 optimal weight: 10.0000 chunk 237 optimal weight: 0.5980 chunk 264 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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** D 394 ASN ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 252 ASN L 670 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23039 Z= 0.302 Angle : 0.630 10.331 31271 Z= 0.321 Chirality : 0.048 0.192 3621 Planarity : 0.004 0.051 3983 Dihedral : 7.519 122.881 3243 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.44 % Allowed : 11.66 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 2896 helix: -0.29 (0.18), residues: 863 sheet: -1.38 (0.25), residues: 421 loop : -1.13 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 231 HIS 0.011 0.001 HIS L 162 PHE 0.028 0.002 PHE D 378 TYR 0.017 0.002 TYR A 130 ARG 0.005 0.000 ARG L 588 *********************** 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 324 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 265 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7376 (p) cc_final: 0.7070 (m) REVERT: M 492 MET cc_start: 0.5426 (tpp) cc_final: 0.4881 (tpp) REVERT: M 592 ASP cc_start: 0.7851 (t0) cc_final: 0.7570 (t0) REVERT: M 641 ILE cc_start: 0.7694 (tt) cc_final: 0.7320 (mt) REVERT: O 200 ILE cc_start: 0.8174 (mm) cc_final: 0.7885 (mm) REVERT: O 332 LEU cc_start: 0.8378 (tp) cc_final: 0.8146 (tp) REVERT: O 560 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5952 (ptp) REVERT: L 464 TYR cc_start: 0.8173 (m-80) cc_final: 0.7930 (m-80) outliers start: 59 outliers final: 39 residues processed: 304 average time/residue: 0.3105 time to fit residues: 151.3278 Evaluate side-chains 276 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 540 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 434 ILE Chi-restraints excluded: chain M residue 517 MET Chi-restraints excluded: chain M residue 526 VAL Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 530 VAL Chi-restraints excluded: chain O residue 560 MET Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 235 CYS Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 overall best weight: 2.5844 ------------------------------------------------------------------------------- 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 201 HIS M 508 GLN 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** L 445 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23039 Z= 0.281 Angle : 0.607 10.004 31271 Z= 0.311 Chirality : 0.048 0.302 3621 Planarity : 0.004 0.053 3983 Dihedral : 7.544 123.544 3243 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.06 % Allowed : 13.60 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2896 helix: -0.19 (0.18), residues: 849 sheet: -1.32 (0.25), residues: 426 loop : -1.13 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 231 HIS 0.010 0.001 HIS L 162 PHE 0.030 0.002 PHE D 378 TYR 0.013 0.001 TYR A 130 ARG 0.005 0.000 ARG L 588 *********************** 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 343 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 269 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.6087 (ttpp) cc_final: 0.4931 (tptt) REVERT: A 457 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.7088 (m) REVERT: M 254 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6947 (tp) REVERT: M 419 MET cc_start: 0.7118 (mmt) cc_final: 0.6844 (mmp) REVERT: M 452 ARG cc_start: 0.5911 (ttt180) cc_final: 0.4974 (ttt-90) REVERT: M 492 MET cc_start: 0.5349 (tpp) cc_final: 0.4899 (tpp) REVERT: M 517 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6168 (ttt) REVERT: M 592 ASP cc_start: 0.7894 (t0) cc_final: 0.7618 (t0) REVERT: M 641 ILE cc_start: 0.7715 (tt) cc_final: 0.7377 (mt) REVERT: O 92 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7151 (m) REVERT: O 200 ILE cc_start: 0.8204 (mm) cc_final: 0.7912 (mm) REVERT: O 472 ILE cc_start: 0.8167 (mt) cc_final: 0.7870 (mm) REVERT: O 560 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6007 (ptp) REVERT: L 464 TYR cc_start: 0.8189 (m-80) cc_final: 0.7916 (m-80) REVERT: L 485 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7099 (pmt170) outliers start: 74 outliers final: 40 residues processed: 321 average time/residue: 0.3158 time to fit residues: 162.3277 Evaluate side-chains 289 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 2.385 ------------------------------------------------------------------------------- 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 283 THR Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 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 526 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 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 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 235 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 23039 Z= 0.471 Angle : 0.737 11.007 31271 Z= 0.382 Chirality : 0.051 0.206 3621 Planarity : 0.005 0.067 3983 Dihedral : 8.030 122.309 3243 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.34 % Allowed : 15.05 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 2896 helix: -0.67 (0.17), residues: 848 sheet: -1.47 (0.25), residues: 426 loop : -1.37 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 231 HIS 0.018 0.002 HIS L 162 PHE 0.038 0.003 PHE D 378 TYR 0.022 0.002 TYR A 130 ARG 0.006 0.001 ARG M 251 *********************** 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 364 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 259 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7236 (mpp) cc_final: 0.6829 (mpp) REVERT: A 457 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.6996 (m) REVERT: A 492 MET cc_start: 0.7726 (ttm) cc_final: 0.7417 (ttm) REVERT: D 81 GLU cc_start: 0.7834 (pt0) cc_final: 0.7560 (mp0) REVERT: D 88 ARG cc_start: 0.6932 (mmm160) cc_final: 0.6174 (mpt180) REVERT: D 237 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6337 (mt-10) REVERT: M 419 MET cc_start: 0.7378 (mmt) cc_final: 0.6486 (mmt) REVERT: M 452 ARG cc_start: 0.5928 (ttt180) cc_final: 0.3065 (tpm170) REVERT: M 492 MET cc_start: 0.5452 (tpp) cc_final: 0.4980 (tpp) REVERT: M 592 ASP cc_start: 0.8040 (t0) cc_final: 0.7757 (t0) REVERT: O 200 ILE cc_start: 0.8318 (mm) cc_final: 0.8072 (mm) REVERT: O 560 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6081 (ptp) REVERT: O 677 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6227 (mm-30) REVERT: L 186 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7869 (t0) REVERT: L 464 TYR cc_start: 0.8177 (m-80) cc_final: 0.7977 (m-80) REVERT: L 516 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6765 (mtm180) outliers start: 105 outliers final: 69 residues processed: 335 average time/residue: 0.3139 time to fit residues: 167.7204 Evaluate side-chains 304 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 232 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 546 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 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 459 GLU 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 551 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 655 ASN 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 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 526 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 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 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 326 VAL 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 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 335 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 491 MET 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 95 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 23 optimal weight: 0.0970 chunk 93 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 252 ASN O 689 ASN L 18 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23039 Z= 0.211 Angle : 0.593 10.778 31271 Z= 0.303 Chirality : 0.046 0.188 3621 Planarity : 0.004 0.056 3983 Dihedral : 7.581 123.486 3243 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.18 % Allowed : 16.70 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2896 helix: -0.30 (0.18), residues: 857 sheet: -1.35 (0.25), residues: 420 loop : -1.21 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 231 HIS 0.009 0.001 HIS M 670 PHE 0.027 0.001 PHE D 378 TYR 0.015 0.001 TYR A 130 ARG 0.005 0.000 ARG A 470 *********************** 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 330 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 253 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7153 (mpp) cc_final: 0.6787 (mpp) REVERT: A 457 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7119 (m) REVERT: D 81 GLU cc_start: 0.7851 (pt0) cc_final: 0.7628 (mp0) REVERT: D 237 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6340 (mt-10) REVERT: M 138 ILE cc_start: 0.4963 (OUTLIER) cc_final: 0.4085 (tp) REVERT: M 419 MET cc_start: 0.7349 (mmt) cc_final: 0.6449 (mmt) REVERT: M 452 ARG cc_start: 0.5872 (ttt180) cc_final: 0.3087 (tpm170) REVERT: M 492 MET cc_start: 0.5396 (tpp) cc_final: 0.4982 (tpp) REVERT: M 592 ASP cc_start: 0.7947 (t0) cc_final: 0.7655 (t0) REVERT: O 200 ILE cc_start: 0.8116 (mm) cc_final: 0.7853 (mm) REVERT: O 560 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6038 (ptp) REVERT: O 677 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6188 (mm-30) REVERT: L 186 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7750 (t0) REVERT: L 464 TYR cc_start: 0.8102 (m-80) cc_final: 0.7899 (m-80) REVERT: L 485 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7099 (pmt170) outliers start: 77 outliers final: 53 residues processed: 310 average time/residue: 0.3195 time to fit residues: 157.8420 Evaluate side-chains 288 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 178 THR Chi-restraints excluded: chain A residue 188 SER 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 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 459 GLU 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 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 434 ILE Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE 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 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 67 VAL 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 235 CYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 ARG Chi-restraints excluded: chain L residue 491 MET Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 23039 Z= 0.504 Angle : 0.762 10.573 31271 Z= 0.391 Chirality : 0.051 0.191 3621 Planarity : 0.006 0.069 3983 Dihedral : 8.113 121.898 3243 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.51 % Allowed : 16.91 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2896 helix: -0.79 (0.17), residues: 865 sheet: -1.51 (0.25), residues: 427 loop : -1.44 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP O 231 HIS 0.019 0.002 HIS L 162 PHE 0.049 0.003 PHE D 378 TYR 0.021 0.002 TYR M 215 ARG 0.007 0.001 ARG O 106 *********************** 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 348 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 239 time to evaluate : 2.490 Fit side-chains REVERT: A 457 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7015 (m) REVERT: D 81 GLU cc_start: 0.7790 (pt0) cc_final: 0.7565 (mp0) REVERT: D 88 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6514 (mpt180) REVERT: D 237 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6445 (mt-10) REVERT: D 648 MET cc_start: 0.7150 (tpp) cc_final: 0.6911 (tpp) REVERT: M 419 MET cc_start: 0.7471 (mmt) cc_final: 0.6462 (mmt) REVERT: M 452 ARG cc_start: 0.5855 (ttt180) cc_final: 0.3113 (tpm170) REVERT: M 492 MET cc_start: 0.5446 (tpp) cc_final: 0.4995 (tpp) REVERT: M 592 ASP cc_start: 0.8100 (t0) cc_final: 0.7820 (t0) REVERT: O 200 ILE cc_start: 0.8291 (mm) cc_final: 0.8043 (mm) REVERT: O 560 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6124 (ptp) REVERT: L 18 GLN cc_start: 0.7365 (mm110) cc_final: 0.7135 (mm-40) REVERT: L 186 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (t0) REVERT: L 419 MET cc_start: 0.7133 (mmm) cc_final: 0.6831 (mmt) REVERT: L 464 TYR cc_start: 0.8252 (m-80) cc_final: 0.7983 (m-80) outliers start: 109 outliers final: 83 residues processed: 316 average time/residue: 0.3121 time to fit residues: 158.2048 Evaluate side-chains 318 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 232 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 ILE 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 401 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 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 551 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 589 VAL 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 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 526 VAL Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 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 184 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 364 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 430 ILE Chi-restraints excluded: chain O residue 517 MET Chi-restraints excluded: chain O residue 530 VAL Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 552 ILE Chi-restraints excluded: chain O residue 560 MET 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 326 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 491 MET Chi-restraints excluded: chain L residue 501 ILE Chi-restraints excluded: chain L residue 504 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 546 THR Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL 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 174 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 M 508 GLN M 679 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23039 Z= 0.177 Angle : 0.591 10.463 31271 Z= 0.300 Chirality : 0.046 0.253 3621 Planarity : 0.004 0.055 3983 Dihedral : 7.506 123.093 3243 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.44 % Allowed : 19.35 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2896 helix: -0.27 (0.18), residues: 871 sheet: -1.27 (0.25), residues: 418 loop : -1.21 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 231 HIS 0.009 0.001 HIS M 670 PHE 0.027 0.001 PHE D 378 TYR 0.013 0.001 TYR A 130 ARG 0.009 0.000 ARG L 516 *********************** 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 323 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 264 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7095 (m) REVERT: D 88 ARG cc_start: 0.6894 (mmm160) cc_final: 0.6365 (mpt180) REVERT: D 237 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6432 (mt-10) REVERT: D 297 TYR cc_start: 0.7884 (t80) cc_final: 0.7593 (t80) REVERT: D 538 MET cc_start: 0.7091 (mmm) cc_final: 0.6859 (mmm) REVERT: M 138 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.3793 (tp) REVERT: M 377 GLU cc_start: 0.5540 (mm-30) cc_final: 0.5327 (mm-30) REVERT: M 419 MET cc_start: 0.7345 (mmt) cc_final: 0.6684 (mmt) REVERT: M 452 ARG cc_start: 0.5885 (ttt180) cc_final: 0.4864 (ttt-90) REVERT: M 492 MET cc_start: 0.5459 (tpp) cc_final: 0.4906 (tpp) REVERT: O 89 TRP cc_start: 0.5214 (m100) cc_final: 0.4973 (m100) REVERT: O 200 ILE cc_start: 0.8039 (mm) cc_final: 0.7771 (mm) REVERT: O 677 GLU cc_start: 0.6853 (tm-30) cc_final: 0.5525 (mm-30) REVERT: L 186 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7731 (t0) REVERT: L 419 MET cc_start: 0.7131 (mmm) cc_final: 0.6901 (mmt) REVERT: L 485 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7093 (pmt170) outliers start: 59 outliers final: 45 residues processed: 305 average time/residue: 0.3164 time to fit residues: 152.8690 Evaluate side-chains 289 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain A residue 178 THR 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 408 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 459 GLU 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 217 VAL 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 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 511 THR Chi-restraints excluded: chain O residue 530 VAL 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 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 530 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 560 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 256 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 237 optimal weight: 0.0570 chunk 248 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN M 119 HIS M 679 HIS ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 689 ASN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 23039 Z= 0.182 Angle : 0.572 8.972 31271 Z= 0.289 Chirality : 0.046 0.219 3621 Planarity : 0.004 0.050 3983 Dihedral : 7.345 122.644 3243 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.19 % Allowed : 19.93 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2896 helix: -0.08 (0.18), residues: 874 sheet: -1.19 (0.25), residues: 423 loop : -1.12 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 404 HIS 0.010 0.001 HIS M 670 PHE 0.021 0.001 PHE D 378 TYR 0.017 0.001 TYR L 464 ARG 0.009 0.000 ARG D 606 *********************** 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 302 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 249 time to evaluate : 3.477 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7146 (m) REVERT: D 88 ARG cc_start: 0.6841 (mmm160) cc_final: 0.6293 (mpt180) REVERT: D 237 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6403 (mt-10) REVERT: D 372 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8057 (mtmm) REVERT: D 538 MET cc_start: 0.6884 (mmm) cc_final: 0.6650 (mmm) REVERT: M 377 GLU cc_start: 0.5443 (mm-30) cc_final: 0.5228 (mm-30) REVERT: M 419 MET cc_start: 0.7271 (mmt) cc_final: 0.6814 (mmt) REVERT: M 452 ARG cc_start: 0.5817 (ttt180) cc_final: 0.4765 (ttt-90) REVERT: M 492 MET cc_start: 0.5384 (tpp) cc_final: 0.4878 (tpp) REVERT: O 89 TRP cc_start: 0.5266 (m100) cc_final: 0.4988 (m100) REVERT: O 92 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.6978 (m) REVERT: O 200 ILE cc_start: 0.7949 (mm) cc_final: 0.7707 (mm) REVERT: O 677 GLU cc_start: 0.6893 (tm-30) cc_final: 0.5529 (mm-30) REVERT: L 186 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7656 (t0) REVERT: L 332 LEU cc_start: 0.7462 (mt) cc_final: 0.7166 (mp) REVERT: L 485 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6951 (pmt170) outliers start: 53 outliers final: 37 residues processed: 287 average time/residue: 0.3344 time to fit residues: 153.3597 Evaluate side-chains 284 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 108 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 D residue 27 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 511 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 186 ASP 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 530 VAL Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 0.5980 chunk 278 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 193 optimal weight: 40.0000 chunk 291 optimal weight: 30.0000 chunk 268 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS M 162 HIS M 679 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23039 Z= 0.220 Angle : 0.588 8.911 31271 Z= 0.297 Chirality : 0.046 0.228 3621 Planarity : 0.004 0.049 3983 Dihedral : 7.345 122.444 3243 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.32 % Allowed : 19.88 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 2896 helix: -0.07 (0.18), residues: 880 sheet: -1.15 (0.25), residues: 423 loop : -1.11 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 404 HIS 0.010 0.001 HIS M 670 PHE 0.028 0.001 PHE D 378 TYR 0.014 0.001 TYR L 691 ARG 0.006 0.000 ARG A 470 ********************** 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 301 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 245 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: A 457 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7167 (m) REVERT: D 88 ARG cc_start: 0.6972 (mmm160) cc_final: 0.6371 (tpp-160) REVERT: D 237 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6355 (mt-10) REVERT: D 538 MET cc_start: 0.6979 (mmm) cc_final: 0.6760 (mmm) REVERT: M 377 GLU cc_start: 0.5300 (mm-30) cc_final: 0.5070 (mm-30) REVERT: M 419 MET cc_start: 0.7352 (mmt) cc_final: 0.6721 (mmt) REVERT: M 492 MET cc_start: 0.5514 (tpp) cc_final: 0.4941 (tpp) REVERT: O 89 TRP cc_start: 0.5315 (m100) cc_final: 0.5019 (m100) REVERT: O 200 ILE cc_start: 0.7995 (mm) cc_final: 0.7733 (mm) REVERT: O 677 GLU cc_start: 0.6748 (tm-30) cc_final: 0.5474 (mm-30) REVERT: L 182 GLN cc_start: 0.7811 (tt0) cc_final: 0.7605 (tt0) REVERT: L 186 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7681 (t0) REVERT: L 332 LEU cc_start: 0.7412 (mt) cc_final: 0.7117 (mp) REVERT: L 485 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6976 (pmt170) outliers start: 56 outliers final: 43 residues processed: 287 average time/residue: 0.3097 time to fit residues: 143.1422 Evaluate side-chains 286 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 401 LEU Chi-restraints excluded: chain O residue 511 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 186 ASP 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 530 VAL Chi-restraints excluded: chain L residue 560 MET Chi-restraints excluded: chain L residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 HIS M 679 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 = 0.4368 r_free = 0.4368 target = 0.179897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145834 restraints weight = 38314.852| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.45 r_work: 0.3812 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23039 Z= 0.221 Angle : 0.590 8.370 31271 Z= 0.298 Chirality : 0.046 0.223 3621 Planarity : 0.004 0.049 3983 Dihedral : 7.322 122.213 3243 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.40 % Allowed : 20.13 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2896 helix: -0.07 (0.18), residues: 881 sheet: -1.13 (0.25), residues: 423 loop : -1.11 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 231 HIS 0.010 0.001 HIS M 670 PHE 0.027 0.001 PHE D 378 TYR 0.019 0.001 TYR L 259 ARG 0.007 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.39 seconds wall clock time: 87 minutes 57.10 seconds (5277.10 seconds total)