Starting phenix.real_space_refine on Sat Feb 17 11:57:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0e_14222/02_2024/7r0e_14222_updated.pdb" } resolution = 2.51 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= 0.001 sd= 0.015 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 53 5.49 5 Mg 2 5.21 5 S 127 5.16 5 C 11420 2.51 5 N 3224 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18554 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: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5778 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 692} Chain breaks: 3 Chain: "C" Number of atoms: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5784 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 29, 'TRANS': 699} Chain breaks: 1 Chain: "M" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 375 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 16} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 377 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 15} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 508 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 508 " occ=0.50 Time building chain proxies: 12.79, per 1000 atoms: 0.69 Number of scatterers: 18554 At special positions: 0 Unit cell: (115.78, 128.185, 124.877, 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 53 15.00 Mg 2 11.99 O 3728 8.00 N 3224 7.00 C 11420 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: 8.26 Conformation dependent library (CDL) restraints added in 4.3 seconds 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 22 sheets defined 43.9% alpha, 12.3% beta 12 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 8.76 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.966A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 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 185 removed outlier: 3.676A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 210 through 217 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 351 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 414 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: 4.018A pdb=" N GLN A 590 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.610A 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: 4.063A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.185A 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 14 through 21 removed outlier: 3.522A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 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 removed outlier: 3.526A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.661A 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 249 through 265 removed outlier: 3.811A 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 345 removed outlier: 4.703A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' 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: 4.122A 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 472 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 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' 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 681 through 697 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: 3.615A 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: 4.066A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.022A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.678A 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 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' 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 272 removed outlier: 4.141A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 391 through 405 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 430 through 438 Processing helix chain 'C' and resid 443 through 449 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 572 Processing helix chain 'C' and resid 575 through 581 Proline residue: C 579 - end of helix Processing helix chain 'C' and resid 586 through 605 removed outlier: 4.810A pdb=" N GLY C 590 " --> 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: 6.852A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.824A 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: 6.721A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 6.633A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR A 567 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR A 540 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.205A 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: 6.950A 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 Processing sheet with id= G, first strand: chain 'B' and resid 178 through 185 removed outlier: 3.565A pdb=" N GLY B 206 " --> pdb=" O PHE B 185 " (cutoff:3.500A) 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: 3.591A 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 removed outlier: 5.708A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) 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 removed outlier: 6.911A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) 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 496 through 498 Processing sheet with id= S, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= T, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.723A pdb=" N GLY C 673 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL C 667 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 722 through 724 removed outlier: 3.636A pdb=" N GLY C 698 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.699A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 8.88 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: 4984 1.33 - 1.45: 3317 1.45 - 1.57: 10269 1.57 - 1.69: 103 1.69 - 1.81: 222 Bond restraints: 18895 Sorted by residual: bond pdb=" C06 K1F M 16 " pdb=" C07 K1F M 16 " ideal model delta sigma weight residual 1.708 1.384 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " ideal model delta sigma weight residual 1.275 1.514 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B GTA M 101 " pdb=" C2B GTA M 101 " ideal model delta sigma weight residual 1.277 1.494 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.541 1.337 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C4' K1F M 16 " pdb=" O4' K1F M 16 " ideal model delta sigma weight residual 1.649 1.449 0.200 2.00e-02 2.50e+03 1.00e+02 ... (remaining 18890 not shown) Histogram of bond angle deviations from ideal: 95.50 - 103.21: 329 103.21 - 110.92: 7020 110.92 - 118.64: 8172 118.64 - 126.35: 9802 126.35 - 134.06: 401 Bond angle restraints: 25724 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 130.29 116.21 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" N1C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 109.68 121.79 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C1A GTA M 101 " pdb=" N9 GTA M 101 " pdb=" C4 GTA M 101 " ideal model delta sigma weight residual 114.98 125.43 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C02 K1F M 16 " pdb=" C04 K1F M 16 " pdb=" N05 K1F M 16 " ideal model delta sigma weight residual 109.58 119.99 -10.41 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O21 GTA M 101 " pdb=" P2 GTA M 101 " pdb=" O22 GTA M 101 " ideal model delta sigma weight residual 109.44 119.68 -10.24 3.00e+00 1.11e-01 1.17e+01 ... (remaining 25719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 11355 34.46 - 68.92: 198 68.92 - 103.37: 27 103.37 - 137.83: 0 137.83 - 172.29: 1 Dihedral angle restraints: 11581 sinusoidal: 5294 harmonic: 6287 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 32.29 -172.29 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA MET B 407 " pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TYR A 540 " pdb=" C TYR A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 11578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2632 0.068 - 0.135: 237 0.135 - 0.203: 3 0.203 - 0.270: 4 0.270 - 0.338: 2 Chirality restraints: 2878 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 -2.81 0.34 2.00e-01 2.50e+01 2.86e+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 -2.74 0.28 2.00e-01 2.50e+01 1.94e+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 -2.69 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2875 not shown) Planarity restraints: 3129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.025 2.00e-02 2.50e+03 1.09e-02 3.24e+00 pdb=" N9 A V 4 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.009 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 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.79e+00 pdb=" N9 A V 7 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.002 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=" C LEU B 271 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 272 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.019 5.00e-02 4.00e+02 ... (remaining 3126 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 171 2.53 - 3.13: 14059 3.13 - 3.72: 30308 3.72 - 4.31: 45040 4.31 - 4.90: 72108 Nonbonded interactions: 161686 Sorted by model distance: nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 801 " model vdw 1.943 2.170 nonbonded pdb="MG MG B 801 " pdb=" O HOH B 930 " model vdw 1.988 2.170 nonbonded pdb=" OE2 GLU A 80 " pdb="MG MG A 801 " model vdw 2.059 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.071 2.440 nonbonded pdb=" OD1 ASN C 301 " pdb=" OG1 THR C 303 " model vdw 2.211 2.440 ... (remaining 161681 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: 3.310 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: 17.670 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 61.290 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.007 0.324 18895 Z= 0.470 Angle : 0.544 14.084 25724 Z= 0.263 Chirality : 0.041 0.338 2878 Planarity : 0.004 0.038 3129 Dihedral : 12.888 172.290 7509 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.15 % Allowed : 3.91 % Favored : 94.94 % 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: 0.63 (0.18), residues: 2149 helix: 1.39 (0.16), residues: 998 sheet: 0.09 (0.33), residues: 251 loop : -0.54 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.002 0.001 HIS A 297 PHE 0.013 0.001 PHE A 520 TYR 0.012 0.001 TYR B 497 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.8215 (mtp) cc_final: 0.7901 (mtp) REVERT: C 457 VAL cc_start: 0.8973 (t) cc_final: 0.8665 (p) outliers start: 22 outliers final: 2 residues processed: 216 average time/residue: 1.8373 time to fit residues: 431.9379 Evaluate side-chains 127 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 146 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18895 Z= 0.296 Angle : 0.581 12.803 25724 Z= 0.292 Chirality : 0.040 0.208 2878 Planarity : 0.004 0.054 3129 Dihedral : 11.422 172.264 3103 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.10 % Allowed : 9.81 % Favored : 89.09 % 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: 2149 helix: 1.51 (0.17), residues: 985 sheet: 0.20 (0.33), residues: 249 loop : -0.47 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 577 HIS 0.002 0.001 HIS C 437 PHE 0.014 0.001 PHE C 420 TYR 0.014 0.001 TYR A 48 ARG 0.015 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7638 (ppp) cc_final: 0.7256 (ppp) REVERT: B 174 MET cc_start: 0.8173 (mmt) cc_final: 0.7860 (mtt) REVERT: C 457 VAL cc_start: 0.9030 (t) cc_final: 0.8527 (p) outliers start: 21 outliers final: 8 residues processed: 137 average time/residue: 1.6536 time to fit residues: 251.0183 Evaluate side-chains 123 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 0.0570 chunk 197 optimal weight: 0.0980 chunk 213 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18895 Z= 0.217 Angle : 0.527 11.714 25724 Z= 0.263 Chirality : 0.039 0.152 2878 Planarity : 0.004 0.044 3129 Dihedral : 11.233 170.895 3103 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.25 % Allowed : 10.39 % Favored : 88.36 % 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: 2149 helix: 1.57 (0.17), residues: 985 sheet: 0.30 (0.34), residues: 242 loop : -0.52 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.002 0.000 HIS A 128 PHE 0.013 0.001 PHE C 656 TYR 0.011 0.001 TYR B 555 ARG 0.010 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 138 average time/residue: 1.6499 time to fit residues: 253.4415 Evaluate side-chains 123 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 132 optimal weight: 0.0060 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 105 ASN B 382 ASN B 456 HIS B 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18895 Z= 0.149 Angle : 0.510 11.604 25724 Z= 0.251 Chirality : 0.038 0.143 2878 Planarity : 0.003 0.035 3129 Dihedral : 11.099 169.023 3101 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.51 % Allowed : 9.92 % Favored : 88.57 % 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: 0.96 (0.18), residues: 2149 helix: 1.71 (0.17), residues: 985 sheet: 0.47 (0.34), residues: 242 loop : -0.47 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.000 HIS B 456 PHE 0.014 0.001 PHE C 656 TYR 0.012 0.001 TYR B 555 ARG 0.008 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7703 (mmm) cc_final: 0.7389 (tpt) REVERT: C 464 LEU cc_start: 0.9056 (mt) cc_final: 0.8854 (mt) REVERT: C 468 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7653 (p) outliers start: 29 outliers final: 7 residues processed: 142 average time/residue: 1.5407 time to fit residues: 243.6813 Evaluate side-chains 122 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.0470 chunk 119 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18895 Z= 0.153 Angle : 0.518 11.607 25724 Z= 0.255 Chirality : 0.038 0.152 2878 Planarity : 0.003 0.035 3129 Dihedral : 11.038 168.464 3101 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.20 % Allowed : 10.75 % Favored : 88.05 % 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: 1.08 (0.18), residues: 2149 helix: 1.80 (0.17), residues: 978 sheet: 0.57 (0.35), residues: 242 loop : -0.39 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.001 0.000 HIS A 128 PHE 0.014 0.001 PHE C 656 TYR 0.011 0.001 TYR B 555 ARG 0.007 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7440 (ptp-170) REVERT: C 464 LEU cc_start: 0.9051 (mt) cc_final: 0.8847 (mt) REVERT: C 468 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7607 (p) REVERT: C 603 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7256 (mmm) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 1.7481 time to fit residues: 259.5890 Evaluate side-chains 129 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18895 Z= 0.197 Angle : 0.526 11.683 25724 Z= 0.257 Chirality : 0.038 0.141 2878 Planarity : 0.003 0.035 3129 Dihedral : 11.016 168.724 3101 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.10 % Allowed : 11.12 % Favored : 87.79 % 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: 1.09 (0.18), residues: 2149 helix: 1.79 (0.17), residues: 979 sheet: 0.55 (0.34), residues: 250 loop : -0.36 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.002 0.000 HIS C 432 PHE 0.013 0.001 PHE C 656 TYR 0.011 0.001 TYR B 555 ARG 0.006 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8086 (ptp-170) REVERT: C 464 LEU cc_start: 0.9071 (mt) cc_final: 0.8857 (mt) REVERT: C 468 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (p) REVERT: C 603 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7268 (mmm) outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 1.5874 time to fit residues: 228.3197 Evaluate side-chains 129 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 153 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 209 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18895 Z= 0.145 Angle : 0.515 11.599 25724 Z= 0.252 Chirality : 0.037 0.151 2878 Planarity : 0.003 0.036 3129 Dihedral : 10.969 167.701 3101 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.10 % Allowed : 11.33 % Favored : 87.58 % 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: 1.09 (0.18), residues: 2149 helix: 1.76 (0.17), residues: 986 sheet: 0.60 (0.34), residues: 248 loop : -0.35 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.000 HIS C 432 PHE 0.014 0.001 PHE C 656 TYR 0.011 0.001 TYR B 657 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.7998 (t0) cc_final: 0.7735 (t0) REVERT: C 3 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8150 (ptp-170) REVERT: C 464 LEU cc_start: 0.9058 (mt) cc_final: 0.8857 (mt) REVERT: C 483 MET cc_start: 0.6197 (mmt) cc_final: 0.5947 (mpp) REVERT: C 603 MET cc_start: 0.7584 (mmt) cc_final: 0.7255 (mmm) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 1.6727 time to fit residues: 251.7073 Evaluate side-chains 127 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 164 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 382 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18895 Z= 0.235 Angle : 0.556 11.724 25724 Z= 0.271 Chirality : 0.039 0.146 2878 Planarity : 0.003 0.043 3129 Dihedral : 10.983 168.559 3101 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.15 % Allowed : 11.74 % Favored : 87.11 % 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: 1.07 (0.18), residues: 2149 helix: 1.76 (0.17), residues: 981 sheet: 0.47 (0.34), residues: 251 loop : -0.34 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.002 0.000 HIS A 297 PHE 0.013 0.001 PHE B 318 TYR 0.012 0.001 TYR B 657 ARG 0.011 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8016 (t0) cc_final: 0.7762 (t0) REVERT: C 3 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7439 (ptp-170) REVERT: C 483 MET cc_start: 0.6334 (mmt) cc_final: 0.6125 (mpp) REVERT: C 603 MET cc_start: 0.7618 (mmt) cc_final: 0.7281 (mmm) outliers start: 22 outliers final: 14 residues processed: 131 average time/residue: 1.6233 time to fit residues: 236.5523 Evaluate side-chains 128 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 0.0070 chunk 184 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 382 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18895 Z= 0.201 Angle : 0.563 12.298 25724 Z= 0.272 Chirality : 0.038 0.145 2878 Planarity : 0.003 0.034 3129 Dihedral : 10.986 168.429 3101 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.99 % Allowed : 12.06 % Favored : 86.95 % 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: 1.02 (0.18), residues: 2149 helix: 1.72 (0.17), residues: 988 sheet: 0.46 (0.34), residues: 252 loop : -0.38 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 449 HIS 0.001 0.000 HIS C 437 PHE 0.013 0.001 PHE C 656 TYR 0.012 0.001 TYR B 657 ARG 0.006 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8031 (t0) cc_final: 0.7770 (t0) REVERT: B 688 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7691 (mpp) REVERT: C 3 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7369 (ptp-170) REVERT: C 483 MET cc_start: 0.6321 (mmt) cc_final: 0.5455 (mpp) REVERT: C 603 MET cc_start: 0.7605 (mmt) cc_final: 0.7288 (mmm) outliers start: 19 outliers final: 12 residues processed: 128 average time/residue: 1.5793 time to fit residues: 224.7381 Evaluate side-chains 125 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 297 HIS ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18895 Z= 0.168 Angle : 0.574 11.795 25724 Z= 0.276 Chirality : 0.038 0.183 2878 Planarity : 0.003 0.047 3129 Dihedral : 10.972 167.943 3101 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.68 % Allowed : 12.47 % Favored : 86.85 % 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: 1.05 (0.18), residues: 2149 helix: 1.75 (0.17), residues: 986 sheet: 0.49 (0.34), residues: 252 loop : -0.36 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.002 0.000 HIS B 184 PHE 0.014 0.001 PHE C 656 TYR 0.013 0.001 TYR B 657 ARG 0.010 0.000 ARG A 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4298 Ramachandran restraints generated. 2149 Oldfield, 0 Emsley, 2149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.7998 (t0) cc_final: 0.7749 (t0) REVERT: B 688 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7624 (mpp) REVERT: C 3 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7962 (ptp-170) REVERT: C 483 MET cc_start: 0.6502 (mmt) cc_final: 0.5684 (mpp) REVERT: C 603 MET cc_start: 0.7582 (mmt) cc_final: 0.7277 (mmm) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 1.6895 time to fit residues: 240.4207 Evaluate side-chains 126 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 25 optimal weight: 0.0040 chunk 47 optimal weight: 0.0170 chunk 172 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 151 optimal weight: 0.5980 overall best weight: 0.2308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047949 restraints weight = 92565.979| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.66 r_work: 0.2916 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18895 Z= 0.138 Angle : 0.564 11.950 25724 Z= 0.272 Chirality : 0.038 0.160 2878 Planarity : 0.003 0.031 3129 Dihedral : 10.922 166.941 3101 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.73 % Allowed : 12.73 % Favored : 86.53 % 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: 1.02 (0.18), residues: 2149 helix: 1.71 (0.17), residues: 993 sheet: 0.48 (0.34), residues: 250 loop : -0.38 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 449 HIS 0.001 0.000 HIS A 713 PHE 0.014 0.001 PHE C 656 TYR 0.012 0.001 TYR B 657 ARG 0.009 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5789.35 seconds wall clock time: 105 minutes 15.42 seconds (6315.42 seconds total)