Starting phenix.real_space_refine on Tue Mar 19 22:25:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqk_40708/03_2024/8sqk_40708_trim_updated.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.029 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 8104 2.51 5 N 2244 2.21 5 O 2833 1.98 5 H 12205 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25550 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 14710 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 929, 14689 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Conformer: "B" Number of residues, atoms: 929, 14689 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} bond proxies already assigned to first conformer: 14856 Chain: "B" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2825 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1153 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2842 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1651 Classifications: {'peptide': 113} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Classifications: {'RNA': 32} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1123 Classifications: {'RNA': 35} Modifications used: {'3*END': 1, 'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna3p': 34} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 169 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'RNA': 2, 'undetermined': 3, 'water': 110} Link IDs: {'rna3p': 1, None: 113} Not linked: pdbres="VSN A1002 " pdbres=" ZN A1003 " Not linked: pdbres=" ZN A1003 " pdbres=" ZN A1004 " Not linked: pdbres=" ZN A1004 " pdbres=" MG A1005 " Not linked: pdbres=" MG A1005 " pdbres="HOH A1101 " Not linked: pdbres="HOH A1101 " pdbres="HOH A1102 " ... (remaining 108 not shown) Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4810 SG CYS A 301 31.985 89.334 110.936 1.00 31.71 S ATOM 4887 SG CYS A 306 33.308 92.664 112.215 1.00 47.50 S ATOM 4952 SG CYS A 310 33.937 89.432 113.971 1.00 30.32 S ATOM 7709 SG CYS A 487 30.472 90.544 89.816 1.00 30.25 S ATOM 10247 SG CYS A 645 30.690 93.996 90.930 1.00 44.42 S ATOM 10257 SG CYS A 646 29.230 91.204 93.185 1.00 39.37 S Time building chain proxies: 18.58, per 1000 atoms: 0.73 Number of scatterers: 25550 At special positions: 0 Unit cell: (94.1775, 137.477, 166.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 72 15.00 Mg 1 11.99 O 2833 8.00 N 2244 7.00 C 8104 6.00 H 12205 1.00 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: 20.58 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " Number of angles added : 6 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2854 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 44.0% alpha, 11.4% beta 30 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 13.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.872A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 5.018A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 236 through 247 Proline residue: A 243 - end of helix removed outlier: 3.899A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.786A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.007A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.952A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.648A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 579 removed outlier: 3.562A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.559A pdb=" N ILE A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.588A pdb=" N GLN A 724 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.859A pdb=" N ASN A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 779 through 788 removed outlier: 3.606A pdb=" N TYR A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.711A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 902 removed outlier: 3.550A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 919 through 925 removed outlier: 4.040A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 919 through 925' Processing helix chain 'B' and resid 7 through 28 removed outlier: 4.630A pdb=" N ALA B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 75 removed outlier: 3.522A pdb=" N LYS B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 97 removed outlier: 3.673A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.764A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.890A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.524A pdb=" N GLN D 19 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 54 through 57 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 106 Processing sheet with id= D, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.578A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= G, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.677A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= I, first strand: chain 'A' and resid 816 through 821 Processing sheet with id= J, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.983A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.741A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.636A pdb=" N ALA G 43 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN G 33 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL G 41 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.691A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 21.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 12172 1.05 - 1.27: 2043 1.27 - 1.48: 6049 1.48 - 1.70: 5434 1.70 - 1.92: 136 Bond restraints: 25834 Sorted by residual: bond pdb=" PB VSN A1002 " pdb=" S1B VSN A1002 " ideal model delta sigma weight residual 1.896 1.508 0.388 2.00e-02 2.50e+03 3.76e+02 bond pdb=" C4' VSN A1001 " pdb=" O4' VSN A1001 " ideal model delta sigma weight residual 1.282 1.611 -0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" O4' VSN A1001 " pdb=" C1' VSN A1001 " ideal model delta sigma weight residual 1.555 1.293 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C3' VSN A1002 " pdb=" C2' VSN A1002 " ideal model delta sigma weight residual 1.291 1.514 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' VSN A1002 " pdb=" N9 VSN A1002 " ideal model delta sigma weight residual 1.296 1.487 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 25829 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.94: 209 102.94 - 111.34: 27597 111.34 - 119.74: 8683 119.74 - 128.14: 9788 128.14 - 136.55: 181 Bond angle restraints: 46458 Sorted by residual: angle pdb=" C THR A 51 " pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta sigma weight residual 120.38 136.55 -16.17 1.37e+00 5.33e-01 1.39e+02 angle pdb=" C THR A 51 " pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta sigma weight residual 110.42 133.59 -23.17 1.99e+00 2.53e-01 1.36e+02 angle pdb=" N LYS A 50 " pdb=" CA LYS A 50 " pdb=" CB LYS A 50 " ideal model delta sigma weight residual 110.46 101.98 8.48 1.55e+00 4.16e-01 2.99e+01 angle pdb=" CA LYS A 50 " pdb=" C LYS A 50 " pdb=" N THR A 51 " ideal model delta sigma weight residual 115.21 121.65 -6.44 1.33e+00 5.65e-01 2.35e+01 angle pdb=" C THR A 51 " pdb=" N ASN A 52 " pdb=" H ASN A 52 " ideal model delta sigma weight residual 124.96 110.48 14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 46453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.95: 11322 18.95 - 37.90: 651 37.90 - 56.85: 255 56.85 - 75.80: 107 75.80 - 94.75: 11 Dihedral angle restraints: 12346 sinusoidal: 7109 harmonic: 5237 Sorted by residual: dihedral pdb=" CA THR A 51 " pdb=" C THR A 51 " pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta harmonic sigma weight residual 180.00 -137.39 -42.61 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" C THR A 51 " pdb=" N THR A 51 " pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta harmonic sigma weight residual -122.00 -143.26 21.26 0 2.50e+00 1.60e-01 7.23e+01 dihedral pdb=" N LYS A 50 " pdb=" C LYS A 50 " pdb=" CA LYS A 50 " pdb=" CB LYS A 50 " ideal model delta harmonic sigma weight residual 122.80 107.44 15.36 0 2.50e+00 1.60e-01 3.78e+01 ... (remaining 12343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2171 0.124 - 0.248: 11 0.248 - 0.371: 1 0.371 - 0.495: 0 0.495 - 0.619: 1 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" P A O 1 " pdb=" OP1 A O 1 " pdb=" OP2 A O 1 " pdb=" O5' A O 1 " both_signs ideal model delta sigma weight residual True 2.41 2.70 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' VSN A1002 " pdb=" C3' VSN A1002 " pdb=" O2' VSN A1002 " pdb=" C1' VSN A1002 " both_signs ideal model delta sigma weight residual False -2.41 -2.62 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2181 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 50 " 0.022 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" N THR A 51 " -0.071 2.00e-02 2.50e+03 pdb=" CA THR A 51 " 0.019 2.00e-02 2.50e+03 pdb=" H THR A 51 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 51 " -0.020 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" N ASN A 52 " 0.059 2.00e-02 2.50e+03 pdb=" CA ASN A 52 " -0.018 2.00e-02 2.50e+03 pdb=" H ASN A 52 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 339 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.024 5.00e-02 4.00e+02 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 719 2.15 - 2.76: 45386 2.76 - 3.37: 67195 3.37 - 3.99: 89798 3.99 - 4.60: 140462 Nonbonded interactions: 343560 Sorted by model distance: nonbonded pdb=" OD1 ASP D 161 " pdb=" H ALA D 162 " model vdw 1.535 1.850 nonbonded pdb=" N ASN G 1 " pdb=" P A O 1 " model vdw 1.601 3.350 nonbonded pdb=" OD1 ASP A 684 " pdb=" HG1 THR A 687 " model vdw 1.605 1.850 nonbonded pdb=" O TYR A 915 " pdb=" HH TYR A 921 " model vdw 1.610 1.850 nonbonded pdb=" OE2 GLU A 254 " pdb=" HH TYR A 286 " model vdw 1.612 1.850 ... (remaining 343555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or (resid 8 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 9 \ through 22 or (resid 23 through 24 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 7 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 27 through 31 or (resid 3 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 34 or (resid 35 through 36 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 37 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.430 Extract box with map and model: 5.100 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 106.210 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.388 13629 Z= 0.513 Angle : 0.613 23.174 18824 Z= 0.337 Chirality : 0.042 0.619 2184 Planarity : 0.004 0.044 2150 Dihedral : 16.116 94.750 5391 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.05 % Allowed : 11.57 % Favored : 86.39 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.21), residues: 1478 helix: 0.48 (0.21), residues: 663 sheet: -0.55 (0.35), residues: 193 loop : -1.81 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 113 PHE 0.017 0.002 PHE A 753 TYR 0.014 0.001 TYR A 831 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASP cc_start: 0.8336 (t70) cc_final: 0.8094 (t0) REVERT: B 38 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2474 (pp) REVERT: C 21 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7337 (mtp180) outliers start: 26 outliers final: 20 residues processed: 188 average time/residue: 0.5869 time to fit residues: 157.9677 Evaluate side-chains 182 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN G 1 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13629 Z= 0.224 Angle : 0.484 5.724 18824 Z= 0.260 Chirality : 0.038 0.157 2184 Planarity : 0.003 0.041 2150 Dihedral : 15.224 94.385 2721 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.75 % Allowed : 10.54 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.69 (0.21), residues: 1478 helix: 0.68 (0.21), residues: 665 sheet: -0.48 (0.34), residues: 200 loop : -1.72 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.002 PHE A 753 TYR 0.013 0.001 TYR A 831 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASP cc_start: 0.8410 (t70) cc_final: 0.8184 (t0) REVERT: A 796 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 73 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7560 (tp40) REVERT: C 21 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7398 (mtp180) REVERT: D 101 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7645 (m-30) outliers start: 35 outliers final: 30 residues processed: 186 average time/residue: 0.5746 time to fit residues: 152.5571 Evaluate side-chains 192 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13629 Z= 0.266 Angle : 0.485 5.471 18824 Z= 0.262 Chirality : 0.038 0.154 2184 Planarity : 0.004 0.061 2150 Dihedral : 15.015 94.452 2719 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.46 % Allowed : 10.23 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.60 (0.21), residues: 1478 helix: 0.78 (0.21), residues: 665 sheet: -0.39 (0.34), residues: 200 loop : -1.74 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.002 PHE D 92 TYR 0.014 0.001 TYR A 831 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: A 477 ASP cc_start: 0.8475 (t70) cc_final: 0.8271 (t0) REVERT: A 796 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: A 905 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 73 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7671 (tp40) REVERT: C 21 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7452 (mtp180) REVERT: C 67 ASP cc_start: 0.6981 (t0) cc_final: 0.6774 (t70) REVERT: D 140 ASN cc_start: 0.7641 (m110) cc_final: 0.7378 (m110) outliers start: 44 outliers final: 31 residues processed: 197 average time/residue: 0.5939 time to fit residues: 165.6304 Evaluate side-chains 198 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13629 Z= 0.193 Angle : 0.452 5.370 18824 Z= 0.242 Chirality : 0.037 0.142 2184 Planarity : 0.003 0.047 2150 Dihedral : 14.806 95.175 2719 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.99 % Allowed : 10.54 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.22), residues: 1478 helix: 1.01 (0.21), residues: 665 sheet: -0.25 (0.35), residues: 201 loop : -1.56 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE A 753 TYR 0.012 0.001 TYR A 831 ARG 0.006 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: A 270 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8402 (mp) REVERT: B 73 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7677 (tp40) REVERT: C 21 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7426 (mtp180) REVERT: C 67 ASP cc_start: 0.6965 (t0) cc_final: 0.6764 (t70) REVERT: D 140 ASN cc_start: 0.7726 (m110) cc_final: 0.7425 (m110) outliers start: 38 outliers final: 29 residues processed: 195 average time/residue: 0.5757 time to fit residues: 161.2327 Evaluate side-chains 194 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13629 Z= 0.267 Angle : 0.481 5.152 18824 Z= 0.259 Chirality : 0.038 0.144 2184 Planarity : 0.004 0.043 2150 Dihedral : 14.752 97.375 2718 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.15 % Allowed : 11.25 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.36 (0.22), residues: 1478 helix: 0.98 (0.21), residues: 665 sheet: -0.19 (0.35), residues: 200 loop : -1.63 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.002 PHE D 92 TYR 0.014 0.001 TYR A 831 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: A 796 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: A 905 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7548 (p) REVERT: B 94 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8337 (mtp) REVERT: C 21 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7398 (mtp180) REVERT: D 140 ASN cc_start: 0.7728 (m110) cc_final: 0.7417 (m110) outliers start: 40 outliers final: 32 residues processed: 191 average time/residue: 0.5609 time to fit residues: 154.9260 Evaluate side-chains 201 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13629 Z= 0.220 Angle : 0.459 5.113 18824 Z= 0.246 Chirality : 0.037 0.140 2184 Planarity : 0.003 0.039 2150 Dihedral : 14.673 99.354 2717 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.70 % Allowed : 11.09 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.22), residues: 1478 helix: 1.10 (0.21), residues: 657 sheet: -0.10 (0.35), residues: 200 loop : -1.55 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 753 TYR 0.012 0.001 TYR A 831 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: A 270 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 796 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: A 905 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7525 (p) REVERT: B 94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: C 21 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7485 (mpp-170) REVERT: D 140 ASN cc_start: 0.7898 (m110) cc_final: 0.7591 (m110) outliers start: 47 outliers final: 33 residues processed: 195 average time/residue: 0.5571 time to fit residues: 157.3030 Evaluate side-chains 201 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13629 Z= 0.217 Angle : 0.456 4.989 18824 Z= 0.244 Chirality : 0.037 0.138 2184 Planarity : 0.003 0.039 2150 Dihedral : 14.606 102.206 2714 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.30 % Allowed : 11.64 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.22), residues: 1478 helix: 1.19 (0.21), residues: 658 sheet: -0.06 (0.35), residues: 200 loop : -1.56 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 753 TYR 0.012 0.001 TYR A 831 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: A 270 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 360 ASN cc_start: 0.8429 (t0) cc_final: 0.8104 (t0) REVERT: A 796 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 905 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7523 (p) REVERT: B 62 MET cc_start: 0.5752 (mmm) cc_final: 0.5509 (mmm) REVERT: B 94 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: C 21 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7330 (mtm180) REVERT: D 52 ASP cc_start: 0.5726 (m-30) cc_final: 0.5264 (m-30) REVERT: D 140 ASN cc_start: 0.7897 (m110) cc_final: 0.7594 (m110) outliers start: 42 outliers final: 33 residues processed: 193 average time/residue: 0.5831 time to fit residues: 161.7591 Evaluate side-chains 203 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13629 Z= 0.314 Angle : 0.496 5.018 18824 Z= 0.267 Chirality : 0.039 0.147 2184 Planarity : 0.004 0.059 2150 Dihedral : 14.609 104.915 2712 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.23 % Allowed : 11.64 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.27 (0.22), residues: 1478 helix: 1.09 (0.21), residues: 657 sheet: -0.10 (0.35), residues: 200 loop : -1.62 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.016 0.002 PHE D 92 TYR 0.015 0.001 TYR A 831 ARG 0.009 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: A 360 ASN cc_start: 0.8442 (t0) cc_final: 0.8107 (t0) REVERT: A 796 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 905 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 94 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: C 21 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7368 (mtm180) REVERT: D 140 ASN cc_start: 0.7719 (m110) cc_final: 0.7440 (m110) outliers start: 41 outliers final: 30 residues processed: 190 average time/residue: 0.5607 time to fit residues: 154.7614 Evaluate side-chains 198 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13629 Z= 0.209 Angle : 0.458 4.883 18824 Z= 0.245 Chirality : 0.037 0.137 2184 Planarity : 0.003 0.051 2150 Dihedral : 14.573 106.434 2712 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.83 % Allowed : 12.20 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.10 (0.22), residues: 1478 helix: 1.24 (0.21), residues: 657 sheet: -0.01 (0.35), residues: 200 loop : -1.54 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE D 92 TYR 0.011 0.001 TYR A 831 ARG 0.007 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: A 360 ASN cc_start: 0.8443 (t0) cc_final: 0.8136 (t0) REVERT: A 905 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7523 (p) REVERT: B 94 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: C 21 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7345 (mtm180) REVERT: D 52 ASP cc_start: 0.5778 (m-30) cc_final: 0.5175 (m-30) REVERT: D 140 ASN cc_start: 0.7896 (m110) cc_final: 0.7614 (m110) outliers start: 36 outliers final: 30 residues processed: 183 average time/residue: 0.5712 time to fit residues: 151.1351 Evaluate side-chains 195 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13629 Z= 0.372 Angle : 0.523 4.961 18824 Z= 0.283 Chirality : 0.041 0.153 2184 Planarity : 0.004 0.049 2150 Dihedral : 14.643 109.125 2712 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.68 % Allowed : 12.43 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1478 helix: 0.95 (0.21), residues: 666 sheet: -0.20 (0.34), residues: 210 loop : -1.71 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.018 0.002 PHE A 753 TYR 0.016 0.002 TYR A 831 ARG 0.006 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: A 905 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7551 (p) REVERT: B 94 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8445 (mtp) REVERT: C 21 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7389 (mtm180) REVERT: D 140 ASN cc_start: 0.7706 (m110) cc_final: 0.7418 (m110) outliers start: 34 outliers final: 30 residues processed: 181 average time/residue: 0.5818 time to fit residues: 151.8341 Evaluate side-chains 192 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 0.0050 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113542 restraints weight = 44438.409| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.94 r_work: 0.2783 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13629 Z= 0.142 Angle : 0.440 4.814 18824 Z= 0.235 Chirality : 0.036 0.142 2184 Planarity : 0.003 0.054 2150 Dihedral : 14.555 109.334 2712 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 12.75 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.03 (0.22), residues: 1478 helix: 1.33 (0.21), residues: 658 sheet: 0.07 (0.35), residues: 198 loop : -1.46 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.001 PHE D 92 TYR 0.010 0.001 TYR A 831 ARG 0.009 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5994.38 seconds wall clock time: 106 minutes 48.34 seconds (6408.34 seconds total)