Starting phenix.real_space_refine on Fri Feb 16 08:19:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szv_10355/02_2024/6szv_10355_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 43 5.49 5 Mg 5 5.21 5 S 92 5.16 5 C 9073 2.51 5 N 2554 2.21 5 O 3080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14847 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 5955 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 bond proxies already assigned to first conformer: 6052 Chain: "C" Number of atoms: 2025 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 2043 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': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "R" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 10} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2KH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 27 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.40 Time building chain proxies: 12.66, per 1000 atoms: 0.85 Number of scatterers: 14847 At special positions: 0 Unit cell: (103.213, 116.216, 112.965, 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 92 16.00 P 43 15.00 Mg 5 11.99 O 3080 8.00 N 2554 7.00 C 9073 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=0, symmetry=0 Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.7 seconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 14 sheets defined 45.5% alpha, 11.6% beta 11 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 7.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 127 through 137 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 Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.074A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.651A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) 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 313 removed outlier: 4.048A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 525 through 532 removed outlier: 4.348A pdb=" N ILE A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 576 through 598 removed outlier: 4.017A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 596 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 4.445A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 removed outlier: 4.083A pdb=" N CYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 712 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.567A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.998A 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 114 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.833A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 263 removed outlier: 4.478A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 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: 4.678A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.670A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 375 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 removed outlier: 5.538A pdb=" N HIS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.595A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 427 " --> pdb=" O VAL 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 removed outlier: 3.593A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 removed outlier: 4.146A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 558 Processing helix chain 'B' and resid 573 through 581 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 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 684 through 697 Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 32 removed outlier: 4.157A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.620A pdb=" N MET C 66 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 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 sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.487A pdb=" N TYR A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY A 121 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.497A pdb=" N ILE A 480 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 498 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 478 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 497 through 501 removed outlier: 6.564A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 614 through 619 removed outlier: 6.486A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= H, first strand: chain 'B' and resid 179 through 193 removed outlier: 3.517A pdb=" N LYS B 198 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.497A pdb=" N VAL B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR B 226 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= K, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= N, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.339A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2335 1.31 - 1.43: 4139 1.43 - 1.56: 8292 1.56 - 1.69: 82 1.69 - 1.81: 162 Bond restraints: 15010 Sorted by residual: bond pdb=" C1' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.561 1.323 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.310 1.533 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' 2KH B 801 " pdb=" N1 2KH B 801 " ideal model delta sigma weight residual 1.322 1.442 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C3' 2KH B 801 " pdb=" C4' 2KH B 801 " ideal model delta sigma weight residual 1.643 1.535 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C4' 2KH B 801 " pdb=" C5' 2KH B 801 " ideal model delta sigma weight residual 1.526 1.426 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 15005 not shown) Histogram of bond angle deviations from ideal: 99.37 - 107.16: 665 107.16 - 114.95: 8984 114.95 - 122.73: 9277 122.73 - 130.52: 1441 130.52 - 138.31: 79 Bond angle restraints: 20446 Sorted by residual: angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 138.31 -12.50 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N LEU B 509 " pdb=" CA LEU B 509 " pdb=" C LEU B 509 " ideal model delta sigma weight residual 109.81 116.34 -6.53 2.21e+00 2.05e-01 8.74e+00 angle pdb=" N MET B 546 " pdb=" CA MET B 546 " pdb=" C MET B 546 " ideal model delta sigma weight residual 111.36 108.20 3.16 1.09e+00 8.42e-01 8.39e+00 angle pdb=" C ILE B 392 " pdb=" N ARG B 393 " pdb=" CA ARG B 393 " ideal model delta sigma weight residual 120.28 124.06 -3.78 1.34e+00 5.57e-01 7.96e+00 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 8638 22.33 - 44.67: 386 44.67 - 67.00: 140 67.00 - 89.33: 24 89.33 - 111.67: 2 Dihedral angle restraints: 9190 sinusoidal: 4237 harmonic: 4953 Sorted by residual: dihedral pdb=" CA ILE B 302 " pdb=" C ILE B 302 " pdb=" N THR B 303 " pdb=" CA THR B 303 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" O1A 2KH B 801 " pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" PB 2KH B 801 " ideal model delta sinusoidal sigma weight residual -34.41 -146.08 111.67 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 9187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1618 0.041 - 0.082: 499 0.082 - 0.123: 116 0.123 - 0.164: 20 0.164 - 0.205: 4 Chirality restraints: 2257 Sorted by residual: chirality pdb=" CA VAL B 348 " pdb=" N VAL B 348 " pdb=" C VAL B 348 " pdb=" CB VAL B 348 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" C1' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" N1 2KH B 801 " pdb=" O4' 2KH B 801 " both_signs ideal model delta sigma weight residual False 2.54 2.36 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 2254 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 620 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 509 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO B 510 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 604 " 0.035 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 605 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.029 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 80 2.39 - 3.02: 7261 3.02 - 3.65: 23599 3.65 - 4.27: 38877 4.27 - 4.90: 60727 Nonbonded interactions: 130544 Sorted by model distance: nonbonded pdb=" O8 M4H A 801 " pdb="MG MG A 802 " model vdw 1.763 2.170 nonbonded pdb=" O ILE A 120 " pdb="MG MG A 803 " model vdw 1.892 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 1.997 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.104 2.170 nonbonded pdb=" O10 M4H A 801 " pdb="MG MG A 802 " model vdw 2.111 2.170 ... (remaining 130539 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.650 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 51.770 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.005 0.238 15010 Z= 0.276 Angle : 0.618 12.498 20446 Z= 0.351 Chirality : 0.042 0.205 2257 Planarity : 0.005 0.059 2472 Dihedral : 14.651 111.666 5986 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 3.65 % Allowed : 4.91 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.79 (0.16), residues: 1688 helix: -1.94 (0.13), residues: 806 sheet: -0.88 (0.37), residues: 176 loop : -1.82 (0.19), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 438 HIS 0.003 0.001 HIS B 32 PHE 0.016 0.002 PHE B 447 TYR 0.013 0.001 TYR B 555 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 336 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.6466 (tpp) cc_final: 0.6137 (tpt) REVERT: A 43 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: A 97 MET cc_start: 0.6883 (tmm) cc_final: 0.6404 (tmt) REVERT: A 116 LYS cc_start: 0.7528 (mmmm) cc_final: 0.7272 (mmtp) REVERT: A 174 ARG cc_start: 0.6943 (tpt90) cc_final: 0.6610 (tpt170) REVERT: A 315 TRP cc_start: 0.7243 (OUTLIER) cc_final: 0.6977 (m-90) REVERT: A 347 GLU cc_start: 0.7262 (pt0) cc_final: 0.6872 (pt0) REVERT: A 418 ILE cc_start: 0.8324 (mm) cc_final: 0.8005 (mm) REVERT: A 485 ARG cc_start: 0.7331 (mmt180) cc_final: 0.6827 (mtp-110) REVERT: A 492 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7714 (ttm170) REVERT: A 543 MET cc_start: 0.7917 (ttm) cc_final: 0.7662 (ttp) REVERT: A 568 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 600 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8337 (pttm) REVERT: A 616 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 48 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 187 LYS cc_start: 0.8014 (mttt) cc_final: 0.7392 (mtmm) REVERT: B 189 LYS cc_start: 0.7513 (pttt) cc_final: 0.6796 (ptpp) REVERT: B 428 GLN cc_start: 0.7837 (mt0) cc_final: 0.7524 (mt0) REVERT: B 567 ASN cc_start: 0.7836 (m-40) cc_final: 0.7629 (m110) REVERT: B 574 LYS cc_start: 0.8264 (mttt) cc_final: 0.7975 (mtpp) REVERT: B 687 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6314 (mmm-85) REVERT: B 691 LYS cc_start: 0.7840 (mttt) cc_final: 0.7635 (mttt) REVERT: B 702 SER cc_start: 0.8268 (p) cc_final: 0.8051 (t) REVERT: C 6 GLU cc_start: 0.6977 (tt0) cc_final: 0.6771 (tt0) REVERT: C 134 LYS cc_start: 0.8372 (mttt) cc_final: 0.8155 (mmtm) REVERT: C 143 LYS cc_start: 0.7398 (mttt) cc_final: 0.7162 (mtpm) REVERT: C 187 LYS cc_start: 0.7980 (tttt) cc_final: 0.7602 (mmtm) REVERT: C 206 MET cc_start: 0.8105 (ttp) cc_final: 0.7819 (ttm) outliers start: 55 outliers final: 20 residues processed: 377 average time/residue: 1.6528 time to fit residues: 670.4929 Evaluate side-chains 301 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 276 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 199 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN A 425 ASN B 58 ASN B 108 GLN B 115 GLN B 124 GLN B 202 GLN B 284 ASN B 313 GLN B 413 ASN B 454 HIS B 465 HIS B 479 GLN B 537 ASN C 138 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15010 Z= 0.144 Angle : 0.462 10.348 20446 Z= 0.240 Chirality : 0.038 0.189 2257 Planarity : 0.004 0.041 2472 Dihedral : 12.765 104.543 2570 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.25 % Allowed : 11.94 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.19), residues: 1688 helix: 0.03 (0.17), residues: 805 sheet: -0.50 (0.37), residues: 179 loop : -1.14 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.003 0.001 HIS B 454 PHE 0.014 0.001 PHE B 551 TYR 0.012 0.001 TYR B 217 ARG 0.004 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: A 7 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5068 (p) REVERT: A 19 LYS cc_start: 0.7283 (mttm) cc_final: 0.6920 (mtpt) REVERT: A 42 MET cc_start: 0.6460 (tpp) cc_final: 0.5960 (tpt) REVERT: A 43 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: A 97 MET cc_start: 0.6777 (tmm) cc_final: 0.6224 (tmt) REVERT: A 116 LYS cc_start: 0.7695 (mmmm) cc_final: 0.7365 (mmtp) REVERT: A 343 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 568 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8379 (tp) REVERT: A 600 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8253 (pttm) REVERT: A 608 ARG cc_start: 0.7556 (mmt90) cc_final: 0.7117 (mmt-90) REVERT: A 616 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8196 (pp) REVERT: B 109 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: B 187 LYS cc_start: 0.8064 (mttt) cc_final: 0.7468 (mtmm) REVERT: B 189 LYS cc_start: 0.7503 (pttt) cc_final: 0.6828 (ptpp) REVERT: B 199 MET cc_start: 0.7885 (mmm) cc_final: 0.7666 (mmt) REVERT: B 290 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7296 (mtt) REVERT: B 428 GLN cc_start: 0.7919 (mt0) cc_final: 0.7561 (mt0) REVERT: B 567 ASN cc_start: 0.7855 (m-40) cc_final: 0.7430 (m110) REVERT: B 569 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: B 574 LYS cc_start: 0.8220 (mttt) cc_final: 0.7996 (mttt) REVERT: B 619 ASP cc_start: 0.6909 (m-30) cc_final: 0.6625 (m-30) REVERT: B 687 ARG cc_start: 0.6569 (mtt180) cc_final: 0.6339 (mmm-85) REVERT: B 691 LYS cc_start: 0.7838 (mttt) cc_final: 0.7527 (mttt) REVERT: C 6 GLU cc_start: 0.6882 (tt0) cc_final: 0.6664 (tt0) REVERT: C 113 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (tmm-80) REVERT: C 134 LYS cc_start: 0.8366 (mttt) cc_final: 0.8090 (mmtm) REVERT: C 187 LYS cc_start: 0.7815 (tttt) cc_final: 0.7482 (mmtm) REVERT: C 206 MET cc_start: 0.8013 (ttp) cc_final: 0.7761 (ttm) REVERT: C 243 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7641 (tm-30) outliers start: 49 outliers final: 17 residues processed: 305 average time/residue: 1.6814 time to fit residues: 553.0777 Evaluate side-chains 284 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 258 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 569 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 425 ASN A 508 ASN A 582 GLN B 124 GLN B 202 GLN B 284 ASN B 413 ASN B 479 GLN C 148 ASN C 182 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15010 Z= 0.199 Angle : 0.487 9.686 20446 Z= 0.254 Chirality : 0.040 0.194 2257 Planarity : 0.004 0.038 2472 Dihedral : 12.474 101.310 2545 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.32 % Allowed : 13.34 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.15 (0.20), residues: 1688 helix: 0.63 (0.18), residues: 815 sheet: -0.21 (0.38), residues: 184 loop : -0.85 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.003 0.001 HIS B 605 PHE 0.018 0.001 PHE A 702 TYR 0.013 0.001 TYR B 217 ARG 0.004 0.000 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 259 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.5467 (OUTLIER) cc_final: 0.4903 (t) REVERT: A 15 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: A 19 LYS cc_start: 0.7269 (mttm) cc_final: 0.6945 (mtpt) REVERT: A 42 MET cc_start: 0.6542 (tpp) cc_final: 0.6026 (tpt) REVERT: A 43 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: A 97 MET cc_start: 0.6875 (tmm) cc_final: 0.6331 (tmt) REVERT: A 116 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7283 (mmtp) REVERT: A 419 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: A 568 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 600 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8247 (pttm) REVERT: A 616 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 109 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: B 187 LYS cc_start: 0.8077 (mttt) cc_final: 0.7434 (mtmm) REVERT: B 189 LYS cc_start: 0.7558 (pttt) cc_final: 0.6873 (ptpp) REVERT: B 199 MET cc_start: 0.7864 (mmm) cc_final: 0.7587 (mmt) REVERT: B 687 ARG cc_start: 0.6614 (mtt180) cc_final: 0.6333 (mmm-85) REVERT: C 113 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8050 (tmm-80) REVERT: C 134 LYS cc_start: 0.8358 (mttt) cc_final: 0.8081 (mmtm) REVERT: C 187 LYS cc_start: 0.7925 (tttt) cc_final: 0.7578 (mmtm) REVERT: C 206 MET cc_start: 0.8043 (ttp) cc_final: 0.7806 (ttm) outliers start: 50 outliers final: 23 residues processed: 286 average time/residue: 1.6203 time to fit residues: 500.7952 Evaluate side-chains 283 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 252 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 241 ASN A 425 ASN B 108 GLN B 124 GLN B 284 ASN B 413 ASN B 479 GLN B 567 ASN B 633 HIS C 13 ASN C 148 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15010 Z= 0.203 Angle : 0.492 9.211 20446 Z= 0.257 Chirality : 0.040 0.203 2257 Planarity : 0.004 0.037 2472 Dihedral : 12.410 99.216 2538 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 14.13 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.23 (0.20), residues: 1688 helix: 0.99 (0.18), residues: 807 sheet: -0.10 (0.38), residues: 185 loop : -0.69 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 363 HIS 0.003 0.001 HIS B 562 PHE 0.018 0.001 PHE A 702 TYR 0.013 0.001 TYR B 217 ARG 0.004 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.5532 (OUTLIER) cc_final: 0.4979 (t) REVERT: A 15 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: A 19 LYS cc_start: 0.7211 (mttm) cc_final: 0.6891 (mtpt) REVERT: A 42 MET cc_start: 0.6509 (tpp) cc_final: 0.5971 (tpt) REVERT: A 43 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: A 84 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7053 (mtp180) REVERT: A 97 MET cc_start: 0.6901 (tmm) cc_final: 0.6361 (tmt) REVERT: A 116 LYS cc_start: 0.7588 (mmmm) cc_final: 0.7214 (mttp) REVERT: A 568 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 600 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8257 (pttm) REVERT: A 616 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8363 (pp) REVERT: B 109 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: B 152 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7873 (mppt) REVERT: B 187 LYS cc_start: 0.8076 (mttt) cc_final: 0.7423 (mtmm) REVERT: B 189 LYS cc_start: 0.7538 (pttt) cc_final: 0.6861 (ptpp) REVERT: B 199 MET cc_start: 0.7848 (mmm) cc_final: 0.7576 (mmt) REVERT: B 687 ARG cc_start: 0.6637 (mtt180) cc_final: 0.6355 (mmm-85) REVERT: C 113 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8101 (tmm-80) REVERT: C 134 LYS cc_start: 0.8370 (mttt) cc_final: 0.8092 (mmtm) REVERT: C 187 LYS cc_start: 0.7959 (tttt) cc_final: 0.7583 (mmtm) REVERT: C 206 MET cc_start: 0.8044 (ttp) cc_final: 0.7812 (ttm) outliers start: 46 outliers final: 25 residues processed: 282 average time/residue: 1.7115 time to fit residues: 520.3585 Evaluate side-chains 284 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 310 ASN B 413 ASN B 567 ASN C 148 ASN C 182 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15010 Z= 0.334 Angle : 0.578 9.814 20446 Z= 0.301 Chirality : 0.044 0.215 2257 Planarity : 0.005 0.047 2472 Dihedral : 12.611 119.079 2533 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.65 % Allowed : 13.74 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.21 (0.20), residues: 1688 helix: 0.93 (0.18), residues: 808 sheet: -0.05 (0.37), residues: 188 loop : -0.67 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 363 HIS 0.004 0.001 HIS A 297 PHE 0.025 0.002 PHE A 702 TYR 0.016 0.002 TYR B 217 ARG 0.006 0.001 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.5409 (OUTLIER) cc_final: 0.4837 (t) REVERT: A 15 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: A 19 LYS cc_start: 0.7254 (mttm) cc_final: 0.6940 (mtpt) REVERT: A 42 MET cc_start: 0.6528 (tpp) cc_final: 0.5985 (tpt) REVERT: A 43 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6348 (tm-30) REVERT: A 84 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7109 (mtp180) REVERT: A 97 MET cc_start: 0.6943 (tmm) cc_final: 0.6374 (tmt) REVERT: A 116 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7220 (mttp) REVERT: A 568 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 600 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8277 (pttm) REVERT: A 616 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 109 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: B 152 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7888 (mppt) REVERT: B 187 LYS cc_start: 0.8073 (mttt) cc_final: 0.7410 (mtmm) REVERT: B 189 LYS cc_start: 0.7587 (pttt) cc_final: 0.6889 (ptpp) REVERT: B 199 MET cc_start: 0.7863 (mmm) cc_final: 0.7641 (mmt) REVERT: B 567 ASN cc_start: 0.7948 (m-40) cc_final: 0.7650 (m110) REVERT: B 569 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: B 687 ARG cc_start: 0.6692 (mtt180) cc_final: 0.6441 (mmm-85) REVERT: C 1 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6681 (mmm) REVERT: C 113 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8106 (tmm-80) REVERT: C 134 LYS cc_start: 0.8406 (mttt) cc_final: 0.8165 (mmtm) outliers start: 55 outliers final: 26 residues processed: 271 average time/residue: 1.7094 time to fit residues: 498.8803 Evaluate side-chains 273 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 569 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 108 GLN B 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15010 Z= 0.141 Angle : 0.456 8.596 20446 Z= 0.239 Chirality : 0.038 0.199 2257 Planarity : 0.003 0.035 2472 Dihedral : 12.409 118.861 2531 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.85 % Allowed : 14.93 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.56 (0.20), residues: 1688 helix: 1.28 (0.19), residues: 806 sheet: 0.07 (0.38), residues: 183 loop : -0.55 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 49 HIS 0.002 0.001 HIS A 297 PHE 0.012 0.001 PHE B 333 TYR 0.009 0.001 TYR B 217 ARG 0.007 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6896 (p0) REVERT: A 15 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: A 19 LYS cc_start: 0.7208 (mttm) cc_final: 0.6884 (mtpt) REVERT: A 42 MET cc_start: 0.6472 (tpp) cc_final: 0.5910 (tpt) REVERT: A 43 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: A 97 MET cc_start: 0.6924 (tmm) cc_final: 0.6361 (tmt) REVERT: A 116 LYS cc_start: 0.7627 (mmmm) cc_final: 0.7385 (mmtp) REVERT: A 598 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7983 (mptp) REVERT: A 600 LYS cc_start: 0.8511 (ptpt) cc_final: 0.8235 (pttm) REVERT: A 608 ARG cc_start: 0.7383 (mmt90) cc_final: 0.7055 (mtm-85) REVERT: A 616 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8323 (pp) REVERT: B 109 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: B 126 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7635 (mmt90) REVERT: B 152 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7864 (mppt) REVERT: B 187 LYS cc_start: 0.8072 (mttt) cc_final: 0.7416 (mtmm) REVERT: B 189 LYS cc_start: 0.7512 (pttt) cc_final: 0.6834 (ptpp) REVERT: B 371 GLU cc_start: 0.7394 (mp0) cc_final: 0.7103 (mp0) REVERT: B 569 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 687 ARG cc_start: 0.6689 (mtt180) cc_final: 0.6412 (mmm-85) REVERT: C 113 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8048 (tmm-80) REVERT: C 134 LYS cc_start: 0.8356 (mttt) cc_final: 0.8081 (mmtm) outliers start: 43 outliers final: 20 residues processed: 270 average time/residue: 1.6418 time to fit residues: 478.4271 Evaluate side-chains 274 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 569 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 108 GLN B 284 ASN B 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15010 Z= 0.405 Angle : 0.622 9.982 20446 Z= 0.323 Chirality : 0.047 0.221 2257 Planarity : 0.005 0.057 2472 Dihedral : 12.593 115.066 2529 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.12 % Allowed : 15.13 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.30 (0.20), residues: 1688 helix: 0.95 (0.18), residues: 807 sheet: -0.02 (0.37), residues: 188 loop : -0.53 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 363 HIS 0.005 0.001 HIS A 227 PHE 0.029 0.002 PHE A 702 TYR 0.017 0.002 TYR B 217 ARG 0.008 0.001 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3366 (ttp) cc_final: 0.2954 (ttm) REVERT: A 7 THR cc_start: 0.5441 (OUTLIER) cc_final: 0.4893 (t) REVERT: A 10 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6876 (p0) REVERT: A 15 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: A 19 LYS cc_start: 0.7226 (mttm) cc_final: 0.6908 (mtpt) REVERT: A 42 MET cc_start: 0.6555 (tpp) cc_final: 0.6266 (tpt) REVERT: A 43 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: A 84 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7079 (mtp180) REVERT: A 97 MET cc_start: 0.6967 (tmm) cc_final: 0.6402 (tmt) REVERT: A 116 LYS cc_start: 0.7588 (mmmm) cc_final: 0.7214 (mttp) REVERT: A 568 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8547 (tp) REVERT: A 600 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8291 (pttm) REVERT: A 616 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 109 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 187 LYS cc_start: 0.8112 (mttt) cc_final: 0.7437 (mtmm) REVERT: B 189 LYS cc_start: 0.7614 (pttt) cc_final: 0.6908 (ptpp) REVERT: B 199 MET cc_start: 0.7809 (mmt) cc_final: 0.7597 (mmt) REVERT: B 670 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7249 (ptt90) REVERT: B 687 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6452 (mmm-85) REVERT: C 113 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8098 (tmm-80) REVERT: C 134 LYS cc_start: 0.8421 (mttt) cc_final: 0.8165 (mmtm) outliers start: 47 outliers final: 25 residues processed: 262 average time/residue: 1.6433 time to fit residues: 464.1097 Evaluate side-chains 269 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 129 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN A 505 HIS B 284 ASN B 567 ASN C 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15010 Z= 0.125 Angle : 0.446 8.415 20446 Z= 0.235 Chirality : 0.038 0.196 2257 Planarity : 0.003 0.036 2472 Dihedral : 12.381 119.316 2529 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.92 % Allowed : 16.72 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1688 helix: 1.40 (0.19), residues: 805 sheet: 0.16 (0.39), residues: 184 loop : -0.45 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 614 HIS 0.002 0.001 HIS B 47 PHE 0.013 0.001 PHE B 333 TYR 0.008 0.001 TYR B 555 ARG 0.008 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3293 (ttp) cc_final: 0.2866 (ttm) REVERT: A 10 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6926 (p0) REVERT: A 15 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: A 19 LYS cc_start: 0.7123 (mttm) cc_final: 0.6799 (mtpt) REVERT: A 42 MET cc_start: 0.6495 (tpp) cc_final: 0.5920 (tpt) REVERT: A 43 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6276 (tm-30) REVERT: A 97 MET cc_start: 0.6909 (tmm) cc_final: 0.6340 (tmt) REVERT: A 116 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7321 (mmtp) REVERT: A 568 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8416 (tp) REVERT: A 600 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8256 (pttm) REVERT: A 608 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7022 (mtm-85) REVERT: B 109 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: B 126 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7637 (mmt90) REVERT: B 187 LYS cc_start: 0.8117 (mttt) cc_final: 0.7446 (mtmm) REVERT: B 189 LYS cc_start: 0.7518 (pttt) cc_final: 0.6841 (ptpp) REVERT: B 371 GLU cc_start: 0.7391 (mp0) cc_final: 0.7050 (mp0) REVERT: B 457 GLU cc_start: 0.7577 (mp0) cc_final: 0.7376 (mp0) REVERT: B 670 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7256 (ptt90) REVERT: B 687 ARG cc_start: 0.6685 (mtt180) cc_final: 0.6395 (mmm-85) REVERT: C 134 LYS cc_start: 0.8364 (mttt) cc_final: 0.8098 (mmtm) outliers start: 29 outliers final: 17 residues processed: 265 average time/residue: 1.6242 time to fit residues: 465.3684 Evaluate side-chains 269 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 247 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 47 optimal weight: 0.2980 chunk 138 optimal weight: 0.0870 chunk 145 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 115 ASN A 425 ASN B 284 ASN B 567 ASN C 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15010 Z= 0.109 Angle : 0.432 8.331 20446 Z= 0.226 Chirality : 0.037 0.169 2257 Planarity : 0.003 0.036 2472 Dihedral : 12.200 116.855 2527 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.06 % Allowed : 16.59 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.99 (0.20), residues: 1688 helix: 1.68 (0.19), residues: 801 sheet: 0.29 (0.39), residues: 184 loop : -0.39 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 614 HIS 0.002 0.001 HIS B 47 PHE 0.010 0.001 PHE A 211 TYR 0.007 0.001 TYR C 205 ARG 0.007 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3420 (ttp) cc_final: 0.3047 (ttm) REVERT: A 7 THR cc_start: 0.5469 (OUTLIER) cc_final: 0.4931 (t) REVERT: A 10 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.7004 (p0) REVERT: A 15 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: A 19 LYS cc_start: 0.7188 (mttm) cc_final: 0.6802 (mtpt) REVERT: A 42 MET cc_start: 0.6478 (tpp) cc_final: 0.5996 (tpt) REVERT: A 43 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: A 97 MET cc_start: 0.6922 (tmm) cc_final: 0.6356 (tmt) REVERT: A 116 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7356 (mmtm) REVERT: A 336 MET cc_start: 0.8443 (mtp) cc_final: 0.8235 (mtt) REVERT: A 343 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 568 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 598 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7921 (mptp) REVERT: A 600 LYS cc_start: 0.8510 (ptpt) cc_final: 0.8242 (pttm) REVERT: B 126 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7640 (mmt90) REVERT: B 187 LYS cc_start: 0.8117 (mttt) cc_final: 0.7447 (mtmm) REVERT: B 189 LYS cc_start: 0.7469 (pttt) cc_final: 0.6810 (ptpp) REVERT: B 371 GLU cc_start: 0.7392 (mp0) cc_final: 0.6979 (mp0) REVERT: B 446 ASP cc_start: 0.7629 (m-30) cc_final: 0.7375 (m-30) REVERT: B 457 GLU cc_start: 0.7573 (mp0) cc_final: 0.7368 (mp0) REVERT: B 616 MET cc_start: 0.8670 (mtt) cc_final: 0.8428 (mtt) REVERT: B 687 ARG cc_start: 0.6674 (mtt180) cc_final: 0.6415 (mmm-85) REVERT: C 134 LYS cc_start: 0.8346 (mttt) cc_final: 0.8083 (mmtm) REVERT: C 171 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7209 (mm-30) outliers start: 31 outliers final: 14 residues processed: 273 average time/residue: 1.5488 time to fit residues: 458.1162 Evaluate side-chains 269 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 112 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 0.0070 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 284 ASN B 567 ASN C 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15010 Z= 0.112 Angle : 0.435 8.801 20446 Z= 0.225 Chirality : 0.037 0.164 2257 Planarity : 0.003 0.034 2472 Dihedral : 12.152 117.102 2525 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.59 % Allowed : 17.45 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1688 helix: 1.72 (0.19), residues: 802 sheet: 0.36 (0.39), residues: 184 loop : -0.33 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 614 HIS 0.002 0.000 HIS B 47 PHE 0.011 0.001 PHE B 185 TYR 0.008 0.001 TYR B 217 ARG 0.007 0.000 ARG B 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3401 (OUTLIER) cc_final: 0.3027 (ttm) REVERT: A 10 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6985 (p0) REVERT: A 15 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: A 19 LYS cc_start: 0.7145 (mttm) cc_final: 0.6812 (mtpt) REVERT: A 42 MET cc_start: 0.6472 (tpp) cc_final: 0.5989 (tpt) REVERT: A 43 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: A 97 MET cc_start: 0.6918 (tmm) cc_final: 0.6345 (tmt) REVERT: A 116 LYS cc_start: 0.7642 (mmmm) cc_final: 0.7337 (mmtp) REVERT: A 343 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 553 MET cc_start: 0.7613 (tpt) cc_final: 0.7345 (tpp) REVERT: A 568 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 600 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8242 (pttm) REVERT: B 126 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7631 (mmt90) REVERT: B 187 LYS cc_start: 0.8108 (mttt) cc_final: 0.7471 (mtmm) REVERT: B 189 LYS cc_start: 0.7465 (pttt) cc_final: 0.6812 (ptpp) REVERT: B 371 GLU cc_start: 0.7385 (mp0) cc_final: 0.6969 (mp0) REVERT: B 446 ASP cc_start: 0.7580 (m-30) cc_final: 0.7336 (m-30) REVERT: B 457 GLU cc_start: 0.7575 (mp0) cc_final: 0.7365 (mp0) REVERT: B 616 MET cc_start: 0.8665 (mtt) cc_final: 0.8421 (mtt) REVERT: B 687 ARG cc_start: 0.6666 (mtt180) cc_final: 0.6436 (mmm-85) REVERT: C 134 LYS cc_start: 0.8330 (mttt) cc_final: 0.8087 (mmtm) REVERT: C 171 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7163 (mm-30) outliers start: 24 outliers final: 15 residues processed: 264 average time/residue: 1.5319 time to fit residues: 438.4147 Evaluate side-chains 265 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 567 ASN C 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118115 restraints weight = 29774.053| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.80 r_work: 0.3056 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15010 Z= 0.215 Angle : 0.517 10.755 20446 Z= 0.266 Chirality : 0.040 0.184 2257 Planarity : 0.004 0.037 2472 Dihedral : 12.292 116.954 2525 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.79 % Allowed : 17.39 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.88 (0.20), residues: 1688 helix: 1.51 (0.19), residues: 804 sheet: 0.26 (0.38), residues: 186 loop : -0.35 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 614 HIS 0.003 0.001 HIS A 227 PHE 0.016 0.002 PHE B 185 TYR 0.014 0.001 TYR B 217 ARG 0.007 0.000 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7591.58 seconds wall clock time: 134 minutes 59.62 seconds (8099.62 seconds total)