Starting phenix.real_space_refine on Wed Apr 10 05:57:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bek_16006/04_2024/8bek_16006_updated.pdb" } resolution = 2.86 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= 0.002 sd= 0.022 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 51 5.49 5 Mg 2 5.21 5 S 127 5.16 5 C 11481 2.51 5 N 3240 2.21 5 O 3734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18635 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 bond proxies already assigned to first conformer: 5865 Chain: "B" Number of atoms: 5854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 732, 5843 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 700} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 732, 5843 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 700} Chain breaks: 2 bond proxies already assigned to first conformer: 5944 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5843 Classifications: {'peptide': 737} Link IDs: {'PTRANS': 29, 'TRANS': 707} Chain: "M" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 508 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 508 " occ=0.50 residue: pdb=" N AARG B 249 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 249 " occ=0.50 Time building chain proxies: 15.82, per 1000 atoms: 0.85 Number of scatterers: 18635 At special positions: 0 Unit cell: (118.371, 127.541, 120.872, 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 127 16.00 P 51 15.00 Mg 2 11.99 O 3734 8.00 N 3240 7.00 C 11481 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 - 3.50 Amino acid : False - 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: 8.10 Conformation dependent library (CDL) restraints added in 5.2 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 44.0% alpha, 12.1% beta 13 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 8.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.979A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 434 through 450 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 581 through 603 removed outlier: 4.494A pdb=" N GLN A 590 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER A 601 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.140A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.126A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.742A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.672A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.658A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.749A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.735A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.703A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.318A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.040A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 473 Processing helix chain 'B' and resid 505 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 678 through 699 removed outlier: 4.267A pdb=" N GLY B 681 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.578A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.959A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.815A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.557A pdb=" N ARG C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 276 through 285 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.516A pdb=" N LYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 566 Processing helix chain 'C' and resid 568 through 571 No H-bonds generated for 'chain 'C' and resid 568 through 571' Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.610A pdb=" N LEU C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 605 removed outlier: 4.486A pdb=" N GLY C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 Proline residue: C 620 - end of helix Processing helix chain 'C' and resid 702 through 704 No H-bonds generated for 'chain 'C' and resid 702 through 704' Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.525A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.632A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.523A pdb=" N GLY A 546 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 619 through 623 removed outlier: 6.817A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.723A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 178 through 184 Processing sheet with id= H, first strand: chain 'B' and resid 225 through 228 Processing sheet with id= I, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.608A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 354 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= N, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= O, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= P, first strand: chain 'C' and resid 322 through 325 Processing sheet with id= Q, first strand: chain 'C' and resid 339 through 345 Processing sheet with id= R, first strand: chain 'C' and resid 332 through 335 removed outlier: 6.825A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 451 through 453 Processing sheet with id= T, first strand: chain 'C' and resid 496 through 498 Processing sheet with id= U, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= V, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.903A pdb=" N GLY C 673 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 667 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 721 through 724 removed outlier: 6.447A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.567A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5172 1.33 - 1.45: 3174 1.45 - 1.57: 10321 1.57 - 1.69: 99 1.69 - 1.81: 222 Bond restraints: 18988 Sorted by residual: bond pdb=" C06 K1F M 16 " pdb=" C07 K1F M 16 " ideal model delta sigma weight residual 1.708 1.387 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " ideal model delta sigma weight residual 1.275 1.507 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1B GTA M 101 " pdb=" C2B GTA M 101 " ideal model delta sigma weight residual 1.277 1.504 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.541 1.331 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C06 K1F M 16 " pdb=" N05 K1F M 16 " ideal model delta sigma weight residual 1.580 1.396 0.184 2.00e-02 2.50e+03 8.49e+01 ... (remaining 18983 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.42: 165 102.42 - 110.32: 4454 110.32 - 118.22: 10220 118.22 - 126.12: 10605 126.12 - 134.02: 402 Bond angle restraints: 25846 Sorted by residual: angle pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 130.29 116.40 13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" N1C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 109.68 121.65 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C1A GTA M 101 " pdb=" C2A GTA M 101 " pdb=" C3A GTA M 101 " ideal model delta sigma weight residual 105.72 94.52 11.20 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N ILE C 147 " pdb=" CA ILE C 147 " pdb=" C ILE C 147 " ideal model delta sigma weight residual 112.96 109.29 3.67 1.00e+00 1.00e+00 1.34e+01 angle pdb=" C02 K1F M 16 " pdb=" C04 K1F M 16 " pdb=" N05 K1F M 16 " ideal model delta sigma weight residual 109.58 120.04 -10.46 3.00e+00 1.11e-01 1.22e+01 ... (remaining 25841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 11440 32.05 - 64.11: 176 64.11 - 96.16: 22 96.16 - 128.21: 0 128.21 - 160.27: 1 Dihedral angle restraints: 11639 sinusoidal: 5299 harmonic: 6340 Sorted by residual: dihedral pdb=" C4' C M 4 " pdb=" C3' C M 4 " pdb=" O3' C M 4 " pdb=" P U M 5 " ideal model delta sinusoidal sigma weight residual -140.00 20.27 -160.27 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" N MET C 202 " pdb=" CA MET C 202 " pdb=" CB MET C 202 " pdb=" CG MET C 202 " ideal model delta sinusoidal sigma weight residual -180.00 -120.27 -59.73 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET B 407 " pdb=" CA MET B 407 " pdb=" CB MET B 407 " pdb=" CG MET B 407 " ideal model delta sinusoidal sigma weight residual -60.00 -118.50 58.50 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 11636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2642 0.065 - 0.131: 233 0.131 - 0.196: 6 0.196 - 0.262: 4 0.262 - 0.327: 3 Chirality restraints: 2888 Sorted by residual: chirality pdb=" C3A GTA M 101 " pdb=" C2A GTA M 101 " pdb=" C4A GTA M 101 " pdb=" O3A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.48 -2.80 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.46 -2.76 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2A GTA M 101 " pdb=" C1A GTA M 101 " pdb=" C3A GTA M 101 " pdb=" O2A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.43 -2.71 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2885 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.026 2.00e-02 2.50e+03 1.18e-02 3.84e+00 pdb=" N9 A V 4 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.019 2.00e-02 2.50e+03 8.72e-03 2.09e+00 pdb=" N9 A V 7 " 0.020 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 8 " -0.019 2.00e-02 2.50e+03 9.63e-03 2.09e+00 pdb=" N1 C R 8 " 0.020 2.00e-02 2.50e+03 pdb=" C2 C R 8 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C R 8 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C R 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C R 8 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C R 8 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C R 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C R 8 " 0.004 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 72 2.40 - 3.03: 11342 3.03 - 3.65: 27276 3.65 - 4.28: 44950 4.28 - 4.90: 74035 Nonbonded interactions: 157675 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O HOH B 905 " model vdw 1.777 2.170 nonbonded pdb="MG MG B 801 " pdb=" O HOH B 919 " model vdw 1.818 2.170 nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 801 " model vdw 1.827 2.170 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 801 " model vdw 1.957 2.170 nonbonded pdb=" OD1 ASN B 306 " pdb=" O HOH B 901 " model vdw 1.986 2.440 ... (remaining 157670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.750 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: 10.460 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 64.750 Find NCS groups from input model: 0.700 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: 0.010 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.006 0.321 18988 Z= 0.388 Angle : 0.513 13.886 25846 Z= 0.251 Chirality : 0.040 0.327 2888 Planarity : 0.003 0.035 3155 Dihedral : 11.683 160.268 7535 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.67 % Allowed : 2.59 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2172 helix: 1.69 (0.17), residues: 975 sheet: 0.23 (0.34), residues: 240 loop : -0.63 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.002 0.001 HIS B 47 PHE 0.014 0.001 PHE C 656 TYR 0.012 0.001 TYR B 555 ARG 0.002 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 271 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8833 (mtp) cc_final: 0.8573 (mtp) REVERT: C 447 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7728 (mp10) outliers start: 13 outliers final: 7 residues processed: 281 average time/residue: 2.0330 time to fit residues: 618.4095 Evaluate side-chains 155 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 607 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 128 HIS A 180 GLN B 137 GLN B 687 GLN C 715 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18988 Z= 0.276 Angle : 0.559 11.374 25846 Z= 0.285 Chirality : 0.041 0.154 2888 Planarity : 0.004 0.048 3155 Dihedral : 11.166 163.481 3112 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.86 % Allowed : 9.16 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2172 helix: 1.66 (0.17), residues: 978 sheet: 0.25 (0.34), residues: 245 loop : -0.67 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.004 0.001 HIS B 47 PHE 0.013 0.001 PHE A 520 TYR 0.013 0.001 TYR B 324 ARG 0.011 0.001 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.8339 (mmt) cc_final: 0.8046 (mmt) REVERT: A 579 MET cc_start: 0.8953 (mtp) cc_final: 0.8720 (mtp) REVERT: C 586 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7958 (tttp) outliers start: 36 outliers final: 11 residues processed: 171 average time/residue: 1.8730 time to fit residues: 352.0244 Evaluate side-chains 147 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 586 LYS Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 708 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 687 GLN C 82 ASN C 447 GLN C 510 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18988 Z= 0.257 Angle : 0.531 11.612 25846 Z= 0.272 Chirality : 0.040 0.139 2888 Planarity : 0.004 0.041 3155 Dihedral : 11.027 166.562 3099 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.60 % Allowed : 9.63 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2172 helix: 1.63 (0.17), residues: 982 sheet: 0.32 (0.34), residues: 238 loop : -0.68 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.013 0.001 PHE A 520 TYR 0.013 0.001 TYR B 324 ARG 0.008 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8973 (mtp) cc_final: 0.8750 (mtp) REVERT: C 508 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7443 (mtm180) outliers start: 31 outliers final: 13 residues processed: 164 average time/residue: 1.7722 time to fit residues: 319.6398 Evaluate side-chains 149 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 708 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 0.1980 chunk 149 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 189 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 687 GLN C 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18988 Z= 0.135 Angle : 0.495 11.572 25846 Z= 0.249 Chirality : 0.038 0.156 2888 Planarity : 0.003 0.037 3155 Dihedral : 10.936 167.974 3099 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.35 % Allowed : 10.30 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2172 helix: 1.72 (0.17), residues: 989 sheet: 0.50 (0.34), residues: 231 loop : -0.69 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 557 HIS 0.002 0.000 HIS A 297 PHE 0.010 0.001 PHE B 333 TYR 0.010 0.001 TYR B 555 ARG 0.009 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8956 (mtp) cc_final: 0.8756 (mtp) REVERT: C 508 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7409 (mtm180) outliers start: 26 outliers final: 7 residues processed: 159 average time/residue: 1.7388 time to fit residues: 305.1687 Evaluate side-chains 141 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 708 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 687 GLN C 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 18988 Z= 0.500 Angle : 0.632 11.445 25846 Z= 0.323 Chirality : 0.045 0.175 2888 Planarity : 0.005 0.055 3155 Dihedral : 11.065 170.792 3095 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.86 % Allowed : 10.97 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2172 helix: 1.30 (0.17), residues: 992 sheet: 0.37 (0.33), residues: 249 loop : -0.86 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 438 HIS 0.005 0.001 HIS B 47 PHE 0.016 0.002 PHE C 420 TYR 0.017 0.002 TYR A 48 ARG 0.008 0.001 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7608 (ptt90) REVERT: B 411 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8033 (mtm) REVERT: C 508 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7408 (mtm180) outliers start: 36 outliers final: 14 residues processed: 159 average time/residue: 1.7093 time to fit residues: 300.3150 Evaluate side-chains 148 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 708 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 687 GLN C 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18988 Z= 0.160 Angle : 0.511 11.491 25846 Z= 0.259 Chirality : 0.039 0.171 2888 Planarity : 0.004 0.045 3155 Dihedral : 10.950 169.018 3095 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.19 % Allowed : 11.80 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2172 helix: 1.52 (0.17), residues: 994 sheet: 0.45 (0.34), residues: 231 loop : -0.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 699 HIS 0.002 0.000 HIS B 47 PHE 0.012 0.001 PHE B 344 TYR 0.011 0.001 TYR B 555 ARG 0.009 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 508 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7370 (mtm180) outliers start: 23 outliers final: 6 residues processed: 150 average time/residue: 1.7197 time to fit residues: 285.2451 Evaluate side-chains 138 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 708 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 119 optimal weight: 0.0170 chunk 178 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18988 Z= 0.146 Angle : 0.506 11.536 25846 Z= 0.255 Chirality : 0.039 0.194 2888 Planarity : 0.003 0.038 3155 Dihedral : 10.874 170.787 3095 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.98 % Allowed : 12.53 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2172 helix: 1.63 (0.17), residues: 996 sheet: 0.55 (0.34), residues: 231 loop : -0.72 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.000 HIS A 128 PHE 0.017 0.001 PHE A 53 TYR 0.011 0.001 TYR B 555 ARG 0.010 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8383 (t80) cc_final: 0.8141 (t80) REVERT: B 411 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7902 (mtm) outliers start: 19 outliers final: 7 residues processed: 145 average time/residue: 1.6900 time to fit residues: 272.7176 Evaluate side-chains 139 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 565 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18988 Z= 0.158 Angle : 0.516 11.518 25846 Z= 0.256 Chirality : 0.039 0.194 2888 Planarity : 0.003 0.036 3155 Dihedral : 10.833 170.984 3095 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.78 % Allowed : 12.84 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2172 helix: 1.66 (0.17), residues: 996 sheet: 0.61 (0.35), residues: 224 loop : -0.71 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.000 HIS B 47 PHE 0.010 0.001 PHE A 191 TYR 0.011 0.001 TYR B 555 ARG 0.007 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8388 (t80) cc_final: 0.8165 (t80) REVERT: B 411 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7835 (mtm) REVERT: C 508 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7369 (mtm180) outliers start: 15 outliers final: 7 residues processed: 142 average time/residue: 1.7103 time to fit residues: 269.0394 Evaluate side-chains 138 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 565 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 196 optimal weight: 0.0040 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18988 Z= 0.132 Angle : 0.514 12.202 25846 Z= 0.251 Chirality : 0.038 0.201 2888 Planarity : 0.003 0.031 3155 Dihedral : 10.773 170.948 3095 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.62 % Allowed : 13.10 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2172 helix: 1.72 (0.17), residues: 997 sheet: 0.67 (0.35), residues: 224 loop : -0.67 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.000 HIS A 52 PHE 0.016 0.001 PHE A 53 TYR 0.011 0.001 TYR B 555 ARG 0.008 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8381 (t80) cc_final: 0.8153 (t80) REVERT: C 508 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7391 (mtm180) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 1.6781 time to fit residues: 264.5182 Evaluate side-chains 139 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 508 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 18 optimal weight: 0.0470 chunk 134 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18988 Z= 0.146 Angle : 0.533 13.076 25846 Z= 0.257 Chirality : 0.038 0.197 2888 Planarity : 0.003 0.040 3155 Dihedral : 10.755 171.309 3095 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.47 % Allowed : 13.15 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2172 helix: 1.73 (0.17), residues: 997 sheet: 0.65 (0.34), residues: 231 loop : -0.65 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.000 HIS B 47 PHE 0.009 0.001 PHE B 333 TYR 0.011 0.001 TYR B 555 ARG 0.006 0.000 ARG B 584 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8396 (t80) cc_final: 0.8155 (t80) REVERT: C 508 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7400 (mtm180) outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 1.6727 time to fit residues: 268.0564 Evaluate side-chains 138 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 chunk 178 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.052874 restraints weight = 107507.143| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.69 r_work: 0.2686 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18988 Z= 0.184 Angle : 0.538 13.047 25846 Z= 0.261 Chirality : 0.039 0.197 2888 Planarity : 0.003 0.035 3155 Dihedral : 10.762 171.598 3095 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.52 % Allowed : 13.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2172 helix: 1.67 (0.17), residues: 997 sheet: 0.60 (0.34), residues: 236 loop : -0.64 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.000 HIS B 47 PHE 0.017 0.001 PHE A 53 TYR 0.011 0.001 TYR B 555 ARG 0.006 0.000 ARG B 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6104.62 seconds wall clock time: 110 minutes 52.02 seconds (6652.02 seconds total)