Starting phenix.real_space_refine on Fri Aug 7 23:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3w_65611/08_2026/9w3w_65611.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.069 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 96 5.16 5 C 14848 2.51 5 N 4408 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24048 Number of models: 1 Model: "" Number of chains: 8 Chain: "1" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 5} Link IDs: {'rna2p': 4} Chain: "2" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 5} Link IDs: {'rna2p': 4} Chain: "3" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 5} Link IDs: {'rna2p': 4} Chain: "4" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 5} Link IDs: {'rna2p': 4} Chain: "A" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5902 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5902 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5902 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5902 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.67, per 1000 atoms: 0.24 Number of scatterers: 24048 At special positions: 0 Unit cell: (121.25, 171.69, 115.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 20 15.00 O 4676 8.00 N 4408 7.00 C 14848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 944.2 milliseconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 12 sheets defined 54.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.594A pdb=" N ASP A 12 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.863A pdb=" N LEU A 20 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.560A pdb=" N GLU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.017A pdb=" N GLY A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.698A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 290 through 311 removed outlier: 3.538A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.763A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.569A pdb=" N LYS A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 434' Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.826A pdb=" N THR A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 501 through 521 removed outlier: 3.671A pdb=" N THR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 551 removed outlier: 3.505A pdb=" N VAL A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 582 through 595 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 610 through 632 removed outlier: 4.325A pdb=" N VAL A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 617 " --> pdb=" O MET A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 Processing helix chain 'A' and resid 639 through 657 Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.964A pdb=" N VAL A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 667 " --> pdb=" O PRO A 663 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.799A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 755 through 770 removed outlier: 3.644A pdb=" N LEU A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.595A pdb=" N ASP B 12 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.863A pdb=" N LEU B 20 " --> pdb=" O ILE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.560A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 149 through 159 removed outlier: 4.018A pdb=" N GLY B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.698A pdb=" N GLY B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 290 through 311 removed outlier: 3.537A pdb=" N VAL B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.763A pdb=" N VAL B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 375 through 381 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.567A pdb=" N LYS B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 434' Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 472 through 475 removed outlier: 3.826A pdb=" N THR B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 475' Processing helix chain 'B' and resid 501 through 521 removed outlier: 3.668A pdb=" N THR B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 3.505A pdb=" N VAL B 536 " --> pdb=" O GLN B 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 610 through 632 removed outlier: 4.325A pdb=" N VAL B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN B 616 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 638 Processing helix chain 'B' and resid 639 through 657 Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.964A pdb=" N VAL B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 667 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.742A pdb=" N ARG B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 724 " --> pdb=" O TYR B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 744 Processing helix chain 'B' and resid 755 through 770 removed outlier: 3.644A pdb=" N LEU B 759 " --> pdb=" O GLY B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 780 through 795 Processing helix chain 'C' and resid 9 through 14 removed outlier: 3.594A pdb=" N ASP C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.863A pdb=" N LEU C 20 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 71 through 83 removed outlier: 3.560A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 149 through 159 removed outlier: 4.017A pdb=" N GLY C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 removed outlier: 3.698A pdb=" N GLY C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 244 through 259 Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 290 through 311 removed outlier: 3.538A pdb=" N VAL C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.763A pdb=" N VAL C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'C' and resid 375 through 381 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.568A pdb=" N LYS C 433 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 434 " --> pdb=" O GLN C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 434' Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 472 through 475 removed outlier: 3.826A pdb=" N THR C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 475' Processing helix chain 'C' and resid 501 through 521 removed outlier: 3.668A pdb=" N THR C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.504A pdb=" N VAL C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 595 Processing helix chain 'C' and resid 598 through 607 Processing helix chain 'C' and resid 610 through 632 removed outlier: 4.325A pdb=" N VAL C 615 " --> pdb=" O ARG C 611 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN C 616 " --> pdb=" O ASP C 612 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 617 " --> pdb=" O MET C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 638 Processing helix chain 'C' and resid 639 through 657 Processing helix chain 'C' and resid 662 through 674 removed outlier: 3.964A pdb=" N VAL C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 667 " --> pdb=" O PRO C 663 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 725 removed outlier: 3.732A pdb=" N ARG C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN C 724 " --> pdb=" O TYR C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 755 through 770 removed outlier: 3.644A pdb=" N LEU C 759 " --> pdb=" O GLY C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 773 No H-bonds generated for 'chain 'C' and resid 771 through 773' Processing helix chain 'C' and resid 780 through 795 Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.594A pdb=" N ASP D 12 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.863A pdb=" N LEU D 20 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 71 through 83 removed outlier: 3.560A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 149 through 159 removed outlier: 4.017A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 189 removed outlier: 3.699A pdb=" N GLY D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 244 through 259 Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 290 through 311 removed outlier: 3.537A pdb=" N VAL D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 3.763A pdb=" N VAL D 334 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY D 336 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'D' and resid 375 through 381 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'D' and resid 418 through 427 Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.567A pdb=" N LYS D 433 " --> pdb=" O GLY D 429 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 434' Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 472 through 475 removed outlier: 3.826A pdb=" N THR D 475 " --> pdb=" O VAL D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 475' Processing helix chain 'D' and resid 501 through 521 removed outlier: 3.668A pdb=" N THR D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.504A pdb=" N VAL D 536 " --> pdb=" O GLN D 532 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 549 " --> pdb=" O ALA D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 595 Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 610 through 632 removed outlier: 4.325A pdb=" N VAL D 615 " --> pdb=" O ARG D 611 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN D 616 " --> pdb=" O ASP D 612 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 617 " --> pdb=" O MET D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 638 Processing helix chain 'D' and resid 639 through 657 Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.964A pdb=" N VAL D 666 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 667 " --> pdb=" O PRO D 663 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 724 removed outlier: 3.902A pdb=" N ARG D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN D 724 " --> pdb=" O TYR D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 744 Processing helix chain 'D' and resid 755 through 770 removed outlier: 3.644A pdb=" N LEU D 759 " --> pdb=" O GLY D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 773 No H-bonds generated for 'chain 'D' and resid 771 through 773' Processing helix chain 'D' and resid 780 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 139 removed outlier: 4.188A pdb=" N ASP A 138 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 3 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N SER A 169 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 5 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 490 removed outlier: 6.833A pdb=" N GLY A 447 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA A 483 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 449 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 485 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 404 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 452 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR A 406 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 454 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 408 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 405 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 528 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 407 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706 removed outlier: 7.340A pdb=" N SER A 705 " --> pdb=" O ARG A 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 139 removed outlier: 4.189A pdb=" N ASP B 138 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 3 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N SER B 169 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL B 5 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 481 through 490 removed outlier: 6.833A pdb=" N GLY B 447 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA B 483 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 449 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 485 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 404 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 452 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR B 406 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 454 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS B 408 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 405 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL B 528 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 407 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 705 through 706 removed outlier: 7.340A pdb=" N SER B 705 " --> pdb=" O ARG B 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 130 through 139 removed outlier: 4.221A pdb=" N ASP C 138 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 3 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER C 169 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL C 5 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 481 through 490 removed outlier: 6.833A pdb=" N GLY C 447 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA C 483 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL C 449 " --> pdb=" O ALA C 483 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 485 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 404 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU C 452 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR C 406 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 454 " --> pdb=" O TYR C 406 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS C 408 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 405 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 528 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 407 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 705 through 706 removed outlier: 7.340A pdb=" N SER C 705 " --> pdb=" O ARG C 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 130 through 139 removed outlier: 4.188A pdb=" N ASP D 138 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 3 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER D 169 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL D 5 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 481 through 490 removed outlier: 6.833A pdb=" N GLY D 447 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA D 483 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL D 449 " --> pdb=" O ALA D 483 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 485 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 404 " --> pdb=" O ASP D 450 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU D 452 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR D 406 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU D 454 " --> pdb=" O TYR D 406 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS D 408 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 405 " --> pdb=" O ALA D 526 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL D 528 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE D 407 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 705 through 706 removed outlier: 7.340A pdb=" N SER D 705 " --> pdb=" O ARG D 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1168 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4234 1.32 - 1.44: 6203 1.44 - 1.56: 13854 1.56 - 1.69: 37 1.69 - 1.81: 156 Bond restraints: 24484 Sorted by residual: bond pdb=" CA LEU B 360 " pdb=" C LEU B 360 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.61e+01 bond pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.58e+01 bond pdb=" C ARG A 415 " pdb=" O ARG A 415 " ideal model delta sigma weight residual 1.244 1.196 0.048 1.00e-02 1.00e+04 2.30e+01 bond pdb=" CA PRO A 416 " pdb=" C PRO A 416 " ideal model delta sigma weight residual 1.517 1.559 -0.042 9.30e-03 1.16e+04 2.01e+01 bond pdb=" C3' A 1 5 " pdb=" O3' A 1 5 " ideal model delta sigma weight residual 1.427 1.478 -0.051 1.20e-02 6.94e+03 1.80e+01 ... (remaining 24479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 32786 2.51 - 5.02: 393 5.02 - 7.53: 49 7.53 - 10.04: 6 10.04 - 12.55: 10 Bond angle restraints: 33244 Sorted by residual: angle pdb=" N LEU C 360 " pdb=" CA LEU C 360 " pdb=" C LEU C 360 " ideal model delta sigma weight residual 112.72 103.31 9.41 1.36e+00 5.41e-01 4.79e+01 angle pdb=" N VAL C 726 " pdb=" CA VAL C 726 " pdb=" C VAL C 726 " ideal model delta sigma weight residual 108.80 116.55 -7.75 1.46e+00 4.69e-01 2.82e+01 angle pdb=" N SER B 733 " pdb=" CA SER B 733 " pdb=" C SER B 733 " ideal model delta sigma weight residual 108.30 116.04 -7.74 1.56e+00 4.11e-01 2.46e+01 angle pdb=" N PRO A 416 " pdb=" CA PRO A 416 " pdb=" C PRO A 416 " ideal model delta sigma weight residual 110.70 116.71 -6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" N LEU B 360 " pdb=" CA LEU B 360 " pdb=" C LEU B 360 " ideal model delta sigma weight residual 110.80 100.62 10.18 2.13e+00 2.20e-01 2.29e+01 ... (remaining 33239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.50: 12847 18.50 - 37.01: 1222 37.01 - 55.51: 379 55.51 - 74.01: 160 74.01 - 92.51: 12 Dihedral angle restraints: 14620 sinusoidal: 5808 harmonic: 8812 Sorted by residual: dihedral pdb=" CA ASP A 316 " pdb=" C ASP A 316 " pdb=" N ASP A 317 " pdb=" CA ASP A 317 " ideal model delta harmonic sigma weight residual 0.00 30.67 -30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ASP C 316 " pdb=" C ASP C 316 " pdb=" N ASP C 317 " pdb=" CA ASP C 317 " ideal model delta harmonic sigma weight residual 0.00 30.67 -30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ASP D 316 " pdb=" C ASP D 316 " pdb=" N ASP D 317 " pdb=" CA ASP D 317 " ideal model delta harmonic sigma weight residual 0.00 30.66 -30.66 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 14617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3359 0.065 - 0.131: 347 0.131 - 0.196: 14 0.196 - 0.261: 3 0.261 - 0.327: 1 Chirality restraints: 3724 Sorted by residual: chirality pdb=" CA ARG C 361 " pdb=" N ARG C 361 " pdb=" C ARG C 361 " pdb=" CB ARG C 361 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA GLU B 541 " pdb=" N GLU B 541 " pdb=" C GLU B 541 " pdb=" CB GLU B 541 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASN B 724 " pdb=" N ASN B 724 " pdb=" C ASN B 724 " pdb=" CB ASN B 724 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3721 not shown) Planarity restraints: 4336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 361 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO A 362 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 361 " -0.095 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO B 362 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 359 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ARG B 359 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG B 359 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 360 " 0.021 2.00e-02 2.50e+03 ... (remaining 4333 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 6 2.25 - 2.91: 9180 2.91 - 3.58: 32485 3.58 - 4.24: 51847 4.24 - 4.90: 90527 Nonbonded interactions: 184045 Sorted by model distance: nonbonded pdb=" P A 3 1 " pdb=" O3' A 3 5 " model vdw 1.591 3.400 nonbonded pdb=" P A 2 1 " pdb=" O3' A 2 5 " model vdw 1.591 3.400 nonbonded pdb=" P A 1 1 " pdb=" O3' A 1 5 " model vdw 1.739 3.400 nonbonded pdb=" OP1 A 1 1 " pdb=" O3' A 1 5 " model vdw 1.792 3.040 nonbonded pdb=" O5' A 1 1 " pdb=" O3' A 1 5 " model vdw 1.926 3.040 ... (remaining 184040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.003 0.068 24484 Z= 0.205 Angle : 0.683 12.553 33244 Z= 0.403 Chirality : 0.040 0.327 3724 Planarity : 0.005 0.147 4336 Dihedral : 17.268 92.515 8988 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.84 % Allowed : 4.05 % Favored : 95.11 % Rotamer: Outliers : 2.30 % Allowed : 18.22 % Favored : 79.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3108 helix: 1.68 (0.14), residues: 1556 sheet: 0.40 (0.27), residues: 312 loop : -1.98 (0.15), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.007 0.001 TYR C 491 PHE 0.009 0.001 PHE D 573 TRP 0.008 0.001 TRP A 395 HIS 0.003 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.20 (24484) covalent geometry : angle 0.68260 / 0.40 (33244) hydrogen bonds : bond 0.16291 / 13.96 ( 1168) hydrogen bonds : angle 4.97576 / 4.24 ( 3432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 0.893 Fit side-chains REVERT: A 125 GLU cc_start: 0.7677 (tp30) cc_final: 0.6879 (mm-30) REVERT: A 164 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7794 (mmt90) REVERT: A 572 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7665 (pt0) REVERT: B 125 GLU cc_start: 0.7674 (tp30) cc_final: 0.6882 (mm-30) REVERT: B 164 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7797 (mmt90) REVERT: B 295 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6180 (tmt170) REVERT: B 572 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7653 (pt0) REVERT: C 125 GLU cc_start: 0.7681 (tp30) cc_final: 0.6880 (mm-30) REVERT: C 164 ARG cc_start: 0.8026 (mmt90) cc_final: 0.7805 (mmt90) REVERT: C 572 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7713 (pt0) REVERT: D 125 GLU cc_start: 0.7682 (tp30) cc_final: 0.6882 (mm-30) REVERT: D 572 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7727 (pt0) outliers start: 55 outliers final: 30 residues processed: 268 average time/residue: 0.8269 time to fit residues: 248.4399 Evaluate side-chains 249 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 727 ARG Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 737 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 ASN B 724 ASN C 730 HIS D 724 ASN D 730 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130507 restraints weight = 23849.187| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.07 r_work: 0.3176 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 24484 Z= 0.112 Angle : 0.557 12.332 33244 Z= 0.283 Chirality : 0.039 0.157 3724 Planarity : 0.004 0.116 4336 Dihedral : 8.050 98.411 3710 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.54 % Favored : 94.88 % Rotamer: Outliers : 2.39 % Allowed : 18.89 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3108 helix: 1.93 (0.14), residues: 1588 sheet: 0.49 (0.26), residues: 348 loop : -1.87 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 361 TYR 0.007 0.001 TYR C 491 PHE 0.005 0.001 PHE C 573 TRP 0.007 0.001 TRP B 395 HIS 0.004 0.001 HIS A 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (24484) covalent geometry : angle 0.55740 / 0.28 (33244) hydrogen bonds : bond 0.04683 / 4.16 ( 1168) hydrogen bonds : angle 4.02803 / 3.50 ( 3432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.896 Fit side-chains REVERT: A 125 GLU cc_start: 0.7666 (tp30) cc_final: 0.6793 (mm-30) REVERT: A 572 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7804 (pt0) REVERT: A 762 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6524 (mtp85) REVERT: B 125 GLU cc_start: 0.7671 (tp30) cc_final: 0.6792 (mm-30) REVERT: B 572 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7793 (pt0) REVERT: B 762 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6521 (mtp85) REVERT: C 125 GLU cc_start: 0.7685 (tp30) cc_final: 0.6820 (mm-30) REVERT: C 572 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7800 (pt0) REVERT: C 762 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6534 (mtp85) REVERT: D 125 GLU cc_start: 0.7670 (tp30) cc_final: 0.6800 (mm-30) REVERT: D 572 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7831 (pt0) REVERT: D 762 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6520 (mtp85) outliers start: 57 outliers final: 15 residues processed: 258 average time/residue: 0.7699 time to fit residues: 224.3003 Evaluate side-chains 223 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 762 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 727 ARG Chi-restraints excluded: chain D residue 762 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 164 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 150 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 GLN D 730 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125597 restraints weight = 23844.337| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.92 r_work: 0.3157 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24484 Z= 0.123 Angle : 0.565 12.954 33244 Z= 0.284 Chirality : 0.040 0.150 3724 Planarity : 0.004 0.100 4336 Dihedral : 7.313 97.925 3664 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.34 % Favored : 95.08 % Rotamer: Outliers : 3.85 % Allowed : 18.93 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3108 helix: 2.07 (0.14), residues: 1576 sheet: 0.49 (0.27), residues: 344 loop : -1.95 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 361 TYR 0.012 0.001 TYR C 491 PHE 0.010 0.001 PHE C 573 TRP 0.009 0.001 TRP B 395 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24484) covalent geometry : angle 0.56515 / 0.28 (33244) hydrogen bonds : bond 0.05044 / 4.51 ( 1168) hydrogen bonds : angle 3.92133 / 3.41 ( 3432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 0.963 Fit side-chains REVERT: A 125 GLU cc_start: 0.7732 (tp30) cc_final: 0.6837 (mm-30) REVERT: A 572 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7883 (pt0) REVERT: A 725 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 762 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6539 (mtp85) REVERT: B 125 GLU cc_start: 0.7753 (tp30) cc_final: 0.6845 (mm-30) REVERT: B 361 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6485 (ttp-110) REVERT: B 572 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7882 (pt0) REVERT: B 762 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6529 (mtp85) REVERT: C 125 GLU cc_start: 0.7759 (tp30) cc_final: 0.6853 (mm-30) REVERT: C 572 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7881 (pt0) REVERT: C 762 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6547 (mtp85) REVERT: D 125 GLU cc_start: 0.7746 (tp30) cc_final: 0.6844 (mm-30) REVERT: D 572 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7899 (pt0) REVERT: D 762 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6538 (mtp85) outliers start: 92 outliers final: 37 residues processed: 276 average time/residue: 0.7567 time to fit residues: 236.1232 Evaluate side-chains 248 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 762 ARG Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 762 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 0.0060 chunk 197 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 288 optimal weight: 0.3980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128675 restraints weight = 23978.249| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.91 r_work: 0.3232 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 24484 Z= 0.096 Angle : 0.509 13.217 33244 Z= 0.255 Chirality : 0.038 0.140 3724 Planarity : 0.003 0.078 4336 Dihedral : 7.083 102.743 3655 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.89 % Favored : 95.56 % Rotamer: Outliers : 2.01 % Allowed : 21.02 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3108 helix: 2.30 (0.14), residues: 1576 sheet: 0.51 (0.27), residues: 344 loop : -1.88 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 723 TYR 0.007 0.001 TYR A 491 PHE 0.005 0.001 PHE A 555 TRP 0.007 0.001 TRP B 395 HIS 0.004 0.001 HIS A 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 (24484) covalent geometry : angle 0.50894 / 0.26 (33244) hydrogen bonds : bond 0.03566 / 3.20 ( 1168) hydrogen bonds : angle 3.78236 / 3.32 ( 3432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.631 Fit side-chains REVERT: A 125 GLU cc_start: 0.7793 (tp30) cc_final: 0.6833 (mm-30) REVERT: A 303 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6839 (mt-10) REVERT: A 490 ASP cc_start: 0.8473 (t0) cc_final: 0.7999 (t0) REVERT: A 572 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7855 (pt0) REVERT: B 125 GLU cc_start: 0.7789 (tp30) cc_final: 0.6825 (mm-30) REVERT: B 490 ASP cc_start: 0.8438 (t0) cc_final: 0.7933 (t0) REVERT: B 572 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7856 (pt0) REVERT: C 125 GLU cc_start: 0.7803 (tp30) cc_final: 0.6851 (mm-30) REVERT: C 303 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6806 (mt-10) REVERT: C 490 ASP cc_start: 0.8423 (t0) cc_final: 0.7968 (t0) REVERT: C 572 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7858 (pt0) REVERT: D 125 GLU cc_start: 0.7801 (tp30) cc_final: 0.6849 (mm-30) REVERT: D 303 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6808 (mt-10) REVERT: D 359 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5862 (mtm-85) REVERT: D 490 ASP cc_start: 0.8475 (t0) cc_final: 0.7991 (t0) REVERT: D 572 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7870 (pt0) outliers start: 48 outliers final: 14 residues processed: 256 average time/residue: 0.7777 time to fit residues: 224.5994 Evaluate side-chains 229 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 226 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 125 optimal weight: 0.0970 chunk 17 optimal weight: 9.9990 chunk 285 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.179643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123580 restraints weight = 23511.790| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.97 r_work: 0.3144 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24484 Z= 0.145 Angle : 0.585 13.297 33244 Z= 0.294 Chirality : 0.042 0.174 3724 Planarity : 0.004 0.080 4336 Dihedral : 7.123 95.354 3655 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.41 % Favored : 95.17 % Rotamer: Outliers : 2.68 % Allowed : 20.39 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3108 helix: 2.21 (0.13), residues: 1568 sheet: 0.41 (0.27), residues: 344 loop : -1.99 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 723 TYR 0.014 0.001 TYR A 491 PHE 0.009 0.001 PHE A 573 TRP 0.008 0.001 TRP B 395 HIS 0.005 0.001 HIS A 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24484) covalent geometry : angle 0.58535 / 0.29 (33244) hydrogen bonds : bond 0.05411 / 4.88 ( 1168) hydrogen bonds : angle 3.85843 / 3.37 ( 3432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.924 Fit side-chains REVERT: A 125 GLU cc_start: 0.7868 (tp30) cc_final: 0.6873 (mm-30) REVERT: A 164 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7739 (mmt-90) REVERT: A 241 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: A 572 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7940 (pt0) REVERT: B 125 GLU cc_start: 0.7863 (tp30) cc_final: 0.6870 (mm-30) REVERT: B 164 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7746 (mmt-90) REVERT: B 241 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: B 572 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7938 (pt0) REVERT: B 613 MET cc_start: 0.8600 (mtp) cc_final: 0.8176 (ttm) REVERT: C 125 GLU cc_start: 0.7874 (tp30) cc_final: 0.6870 (mm-30) REVERT: C 164 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7744 (mmt-90) REVERT: C 241 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: D 125 GLU cc_start: 0.7852 (tp30) cc_final: 0.6862 (mm-30) REVERT: D 164 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7735 (mmt-90) REVERT: D 241 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: D 359 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5826 (mtm-85) REVERT: D 613 MET cc_start: 0.8609 (mtp) cc_final: 0.8187 (ttm) outliers start: 64 outliers final: 25 residues processed: 246 average time/residue: 0.7787 time to fit residues: 216.5876 Evaluate side-chains 226 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 192 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN D 651 HIS D 655 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127285 restraints weight = 23634.999| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.83 r_work: 0.2957 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24484 Z= 0.213 Angle : 0.714 13.516 33244 Z= 0.359 Chirality : 0.046 0.217 3724 Planarity : 0.005 0.074 4336 Dihedral : 7.345 89.065 3654 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Rotamer: Outliers : 3.56 % Allowed : 19.89 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3108 helix: 1.69 (0.13), residues: 1584 sheet: 0.32 (0.27), residues: 348 loop : -2.09 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 422 TYR 0.016 0.002 TYR C 491 PHE 0.010 0.002 PHE B 218 TRP 0.011 0.002 TRP C 395 HIS 0.007 0.001 HIS C 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (24484) covalent geometry : angle 0.71432 / 0.36 (33244) hydrogen bonds : bond 0.07374 / 6.66 ( 1168) hydrogen bonds : angle 4.06787 / 3.55 ( 3432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 0.903 Fit side-chains REVERT: A 125 GLU cc_start: 0.7841 (tp30) cc_final: 0.6836 (mm-30) REVERT: A 164 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (mmt-90) REVERT: A 241 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: A 613 MET cc_start: 0.8726 (mtp) cc_final: 0.8316 (ttm) REVERT: A 762 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6683 (mpp80) REVERT: B 125 GLU cc_start: 0.7852 (tp30) cc_final: 0.6829 (mm-30) REVERT: B 164 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7868 (mmt-90) REVERT: B 241 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: B 355 LYS cc_start: 0.6844 (ttpt) cc_final: 0.6440 (ptmt) REVERT: B 361 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6416 (ttp-110) REVERT: B 613 MET cc_start: 0.8712 (mtp) cc_final: 0.8329 (ttm) REVERT: B 762 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6659 (mpp80) REVERT: C 125 GLU cc_start: 0.7834 (tp30) cc_final: 0.6840 (mm-30) REVERT: C 164 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (mmt-90) REVERT: C 241 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: C 613 MET cc_start: 0.8723 (mtp) cc_final: 0.8306 (ttm) REVERT: C 762 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6668 (mpp80) REVERT: D 125 GLU cc_start: 0.7833 (tp30) cc_final: 0.6844 (mm-30) REVERT: D 164 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7865 (mmt-90) REVERT: D 241 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: D 359 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5862 (mtm-85) REVERT: D 613 MET cc_start: 0.8726 (mtp) cc_final: 0.8339 (ttm) REVERT: D 762 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6667 (mpp80) outliers start: 85 outliers final: 40 residues processed: 263 average time/residue: 0.7198 time to fit residues: 214.9408 Evaluate side-chains 240 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 762 ARG Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 762 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 651 HIS A 655 GLN B 345 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 651 HIS C 655 GLN D 345 GLN D 651 HIS D 655 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128164 restraints weight = 23560.377| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.74 r_work: 0.2987 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24484 Z= 0.172 Angle : 0.640 13.158 33244 Z= 0.323 Chirality : 0.043 0.188 3724 Planarity : 0.005 0.073 4336 Dihedral : 7.333 93.240 3654 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.02 % Favored : 94.69 % Rotamer: Outliers : 4.02 % Allowed : 19.93 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3108 helix: 1.73 (0.13), residues: 1584 sheet: 0.29 (0.27), residues: 348 loop : -2.08 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 723 TYR 0.014 0.002 TYR A 491 PHE 0.010 0.001 PHE D 573 TRP 0.011 0.001 TRP A 395 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (24484) covalent geometry : angle 0.63965 / 0.32 (33244) hydrogen bonds : bond 0.06355 / 5.73 ( 1168) hydrogen bonds : angle 4.00124 / 3.51 ( 3432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 188 time to evaluate : 0.701 Fit side-chains REVERT: A 125 GLU cc_start: 0.7807 (tp30) cc_final: 0.6759 (mm-30) REVERT: A 149 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7209 (t0) REVERT: A 164 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7796 (mmt-90) REVERT: A 613 MET cc_start: 0.8682 (mtp) cc_final: 0.8052 (ttm) REVERT: B 125 GLU cc_start: 0.7812 (tp30) cc_final: 0.6748 (mm-30) REVERT: B 149 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (t0) REVERT: B 164 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7808 (mmt-90) REVERT: B 361 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6368 (ttp-110) REVERT: B 613 MET cc_start: 0.8669 (mtp) cc_final: 0.8066 (ttm) REVERT: C 125 GLU cc_start: 0.7801 (tp30) cc_final: 0.6763 (mm-30) REVERT: C 149 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7206 (t0) REVERT: C 164 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7805 (mmt-90) REVERT: C 613 MET cc_start: 0.8683 (mtp) cc_final: 0.8048 (ttm) REVERT: D 125 GLU cc_start: 0.7795 (tp30) cc_final: 0.6766 (mm-30) REVERT: D 149 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7214 (t0) REVERT: D 164 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7807 (mmt-90) REVERT: D 359 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5814 (mtm-85) REVERT: D 613 MET cc_start: 0.8684 (mtp) cc_final: 0.8085 (ttm) outliers start: 96 outliers final: 47 residues processed: 267 average time/residue: 0.7156 time to fit residues: 217.2167 Evaluate side-chains 237 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 620 CYS Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 43 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.178869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123050 restraints weight = 23565.745| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.94 r_work: 0.3142 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24484 Z= 0.127 Angle : 0.565 13.069 33244 Z= 0.287 Chirality : 0.041 0.148 3724 Planarity : 0.004 0.064 4336 Dihedral : 7.241 97.998 3654 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.05 % Favored : 94.53 % Rotamer: Outliers : 2.93 % Allowed : 21.02 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3108 helix: 1.94 (0.13), residues: 1584 sheet: 0.37 (0.28), residues: 308 loop : -1.99 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.011 0.001 TYR A 491 PHE 0.012 0.001 PHE A 573 TRP 0.011 0.001 TRP D 395 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (24484) covalent geometry : angle 0.56507 / 0.29 (33244) hydrogen bonds : bond 0.05038 / 4.54 ( 1168) hydrogen bonds : angle 3.90987 / 3.44 ( 3432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 0.906 Fit side-chains REVERT: A 21 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6169 (tppt) REVERT: A 125 GLU cc_start: 0.7812 (tp30) cc_final: 0.6767 (mm-30) REVERT: A 149 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 164 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7696 (mmt-90) REVERT: A 490 ASP cc_start: 0.8544 (t0) cc_final: 0.8256 (t0) REVERT: A 613 MET cc_start: 0.8677 (mtp) cc_final: 0.8229 (ttm) REVERT: B 21 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6156 (tppt) REVERT: B 65 LYS cc_start: 0.7821 (mmpt) cc_final: 0.7385 (mtmm) REVERT: B 125 GLU cc_start: 0.7811 (tp30) cc_final: 0.6764 (mm-30) REVERT: B 149 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7180 (t0) REVERT: B 164 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7711 (mmt-90) REVERT: B 490 ASP cc_start: 0.8554 (t0) cc_final: 0.8265 (t0) REVERT: B 613 MET cc_start: 0.8653 (mtp) cc_final: 0.8227 (ttm) REVERT: C 21 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6133 (tppt) REVERT: C 125 GLU cc_start: 0.7809 (tp30) cc_final: 0.6768 (mm-30) REVERT: C 149 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7157 (t0) REVERT: C 164 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7718 (mmt-90) REVERT: C 490 ASP cc_start: 0.8565 (t0) cc_final: 0.8274 (t0) REVERT: C 613 MET cc_start: 0.8673 (mtp) cc_final: 0.8215 (ttm) REVERT: D 21 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6185 (tppt) REVERT: D 125 GLU cc_start: 0.7794 (tp30) cc_final: 0.6758 (mm-30) REVERT: D 149 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7184 (t0) REVERT: D 164 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7750 (mmt-90) REVERT: D 359 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5777 (mtm-85) REVERT: D 490 ASP cc_start: 0.8559 (t0) cc_final: 0.8275 (t0) REVERT: D 613 MET cc_start: 0.8667 (mtp) cc_final: 0.8245 (ttm) outliers start: 70 outliers final: 38 residues processed: 241 average time/residue: 0.7381 time to fit residues: 201.5942 Evaluate side-chains 244 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 620 CYS Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 305 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN B 651 HIS B 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120891 restraints weight = 23737.151| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.92 r_work: 0.3116 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24484 Z= 0.164 Angle : 0.620 13.049 33244 Z= 0.313 Chirality : 0.043 0.182 3724 Planarity : 0.005 0.062 4336 Dihedral : 7.267 93.731 3654 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.47 % Favored : 94.18 % Rotamer: Outliers : 2.76 % Allowed : 21.27 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3108 helix: 1.85 (0.13), residues: 1580 sheet: 0.31 (0.26), residues: 348 loop : -2.06 (0.15), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 723 TYR 0.014 0.002 TYR A 491 PHE 0.009 0.001 PHE B 573 TRP 0.010 0.001 TRP A 395 HIS 0.005 0.001 HIS C 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (24484) covalent geometry : angle 0.61991 / 0.31 (33244) hydrogen bonds : bond 0.06015 / 5.43 ( 1168) hydrogen bonds : angle 3.95538 / 3.47 ( 3432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.886 Fit side-chains REVERT: A 21 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6176 (tppt) REVERT: A 125 GLU cc_start: 0.7832 (tp30) cc_final: 0.6786 (mm-30) REVERT: A 149 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 164 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7827 (mmt-90) REVERT: A 613 MET cc_start: 0.8688 (mtp) cc_final: 0.8249 (ttm) REVERT: B 21 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6142 (tppt) REVERT: B 125 GLU cc_start: 0.7833 (tp30) cc_final: 0.6775 (mm-30) REVERT: B 149 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7226 (t0) REVERT: B 164 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7842 (mmt-90) REVERT: B 613 MET cc_start: 0.8667 (mtp) cc_final: 0.8250 (ttm) REVERT: C 21 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6146 (tppt) REVERT: C 125 GLU cc_start: 0.7822 (tp30) cc_final: 0.6787 (mm-30) REVERT: C 149 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7206 (t0) REVERT: C 164 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (mmt-90) REVERT: C 613 MET cc_start: 0.8684 (mtp) cc_final: 0.8239 (ttm) REVERT: D 21 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6155 (tppt) REVERT: D 125 GLU cc_start: 0.7809 (tp30) cc_final: 0.6786 (mm-30) REVERT: D 149 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7222 (t0) REVERT: D 164 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (mmt-90) REVERT: D 359 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.5794 (mtm-85) REVERT: D 613 MET cc_start: 0.8679 (mtp) cc_final: 0.8265 (ttm) outliers start: 66 outliers final: 44 residues processed: 240 average time/residue: 0.7156 time to fit residues: 194.1070 Evaluate side-chains 235 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 620 CYS Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 200 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN B 651 HIS B 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125503 restraints weight = 23718.950| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.96 r_work: 0.3169 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24484 Z= 0.108 Angle : 0.529 12.969 33244 Z= 0.268 Chirality : 0.039 0.143 3724 Planarity : 0.004 0.052 4336 Dihedral : 7.109 100.672 3654 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.47 % Favored : 95.11 % Rotamer: Outliers : 1.93 % Allowed : 22.03 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3108 helix: 2.10 (0.13), residues: 1580 sheet: 0.34 (0.27), residues: 344 loop : -1.96 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 762 TYR 0.009 0.001 TYR B 720 PHE 0.010 0.001 PHE A 573 TRP 0.010 0.001 TRP A 395 HIS 0.003 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (24484) covalent geometry : angle 0.52882 / 0.27 (33244) hydrogen bonds : bond 0.04166 / 3.75 ( 1168) hydrogen bonds : angle 3.82910 / 3.39 ( 3432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 2.649 Fit side-chains REVERT: A 125 GLU cc_start: 0.7804 (tp30) cc_final: 0.6815 (mm-30) REVERT: A 149 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7224 (t0) REVERT: A 490 ASP cc_start: 0.8480 (t0) cc_final: 0.7912 (t0) REVERT: A 613 MET cc_start: 0.8656 (mtp) cc_final: 0.7975 (ttm) REVERT: A 762 ARG cc_start: 0.7255 (tpp80) cc_final: 0.6912 (mpp80) REVERT: B 21 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6278 (tppt) REVERT: B 125 GLU cc_start: 0.7808 (tp30) cc_final: 0.6806 (mm-30) REVERT: B 149 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7240 (t0) REVERT: B 490 ASP cc_start: 0.8492 (t0) cc_final: 0.7928 (t0) REVERT: B 572 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7933 (pt0) REVERT: B 613 MET cc_start: 0.8632 (mtp) cc_final: 0.7973 (ttm) REVERT: B 762 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6909 (mpp80) REVERT: C 21 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6249 (tppt) REVERT: C 125 GLU cc_start: 0.7795 (tp30) cc_final: 0.6819 (mm-30) REVERT: C 149 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7205 (t0) REVERT: C 490 ASP cc_start: 0.8495 (t0) cc_final: 0.7931 (t0) REVERT: C 613 MET cc_start: 0.8650 (mtp) cc_final: 0.7962 (ttm) REVERT: C 762 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6913 (mpp80) REVERT: D 21 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6305 (tppt) REVERT: D 125 GLU cc_start: 0.7782 (tp30) cc_final: 0.6810 (mm-30) REVERT: D 149 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7245 (t0) REVERT: D 359 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5859 (mtm-85) REVERT: D 490 ASP cc_start: 0.8498 (t0) cc_final: 0.7931 (t0) REVERT: D 613 MET cc_start: 0.8644 (mtp) cc_final: 0.7988 (ttm) REVERT: D 762 ARG cc_start: 0.7257 (tpp80) cc_final: 0.6913 (mpp80) outliers start: 46 outliers final: 29 residues processed: 243 average time/residue: 0.7764 time to fit residues: 212.6321 Evaluate side-chains 238 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 408 CYS Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 778 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 262 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 227 optimal weight: 0.5980 chunk 299 optimal weight: 0.3980 chunk 234 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN B 651 HIS B 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125110 restraints weight = 23717.831| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.94 r_work: 0.3170 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24484 Z= 0.109 Angle : 0.531 12.812 33244 Z= 0.268 Chirality : 0.039 0.142 3724 Planarity : 0.004 0.047 4336 Dihedral : 7.001 98.647 3653 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.54 % Favored : 95.05 % Rotamer: Outliers : 1.84 % Allowed : 22.19 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3108 helix: 2.17 (0.13), residues: 1580 sheet: 0.40 (0.27), residues: 344 loop : -1.94 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 762 TYR 0.010 0.001 TYR A 491 PHE 0.009 0.001 PHE B 573 TRP 0.010 0.001 TRP A 395 HIS 0.003 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (24484) covalent geometry : angle 0.53058 / 0.27 (33244) hydrogen bonds : bond 0.04282 / 3.87 ( 1168) hydrogen bonds : angle 3.78698 / 3.35 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9166.26 seconds wall clock time: 156 minutes 17.20 seconds (9377.20 seconds total)