Starting phenix.real_space_refine on Tue Apr 7 03:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3w_65611/04_2026/9w3w_65611_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3w_65611/04_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_65611/04_2026/9w3w_65611_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3w_65611/04_2026/9w3w_65611_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w3w_65611/04_2026/9w3w_65611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3w_65611/04_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 5.40, per 1000 atoms: 0.22 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: 1.91 Conformation dependent library (CDL) restraints added in 891.5 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: 0.92 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: 4.06 Time building geometry restraints manager: 2.41 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=" CA ARG A 415 " pdb=" C ARG A 415 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.23e-02 6.61e+03 1.23e+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: 3354 0.065 - 0.131: 352 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.850 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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= 0.201 Angle : 0.682 12.553 33244 Z= 0.403 Chirality : 0.041 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 covalent geometry : bond 0.00316 (24484) covalent geometry : angle 0.68190 (33244) hydrogen bonds : bond 0.16291 ( 1168) hydrogen bonds : angle 4.97576 ( 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 : 0.853 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: 0.7664 (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: 0.7926 time to fit residues: 237.1354 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 : 0.808 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4063 r_free = 0.4063 target = 0.182948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127821 restraints weight = 23795.852| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.85 r_work: 0.3198 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 24484 Z= 0.114 Angle : 0.558 13.555 33244 Z= 0.282 Chirality : 0.039 0.182 3724 Planarity : 0.004 0.104 4336 Dihedral : 7.924 102.645 3710 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.34 % Favored : 95.08 % Rotamer: Outliers : 2.43 % Allowed : 18.68 % Favored : 78.89 % 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: 0.55 (0.15), residues: 3108 helix: 1.88 (0.14), residues: 1600 sheet: 0.46 (0.26), residues: 344 loop : -1.93 (0.15), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 361 TYR 0.010 0.001 TYR C 491 PHE 0.006 0.001 PHE C 555 TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS D 730 Details of bonding type rmsd covalent geometry : bond 0.00225 (24484) covalent geometry : angle 0.55772 (33244) hydrogen bonds : bond 0.04470 ( 1168) hydrogen bonds : angle 3.95187 ( 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 280 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.843 Fit side-chains REVERT: A 125 GLU cc_start: 0.7627 (tp30) cc_final: 0.6811 (mm-30) REVERT: A 490 ASP cc_start: 0.8427 (t0) cc_final: 0.7826 (t0) REVERT: A 572 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7852 (pt0) REVERT: B 125 GLU cc_start: 0.7631 (tp30) cc_final: 0.6811 (mm-30) REVERT: B 572 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7843 (pt0) REVERT: C 125 GLU cc_start: 0.7645 (tp30) cc_final: 0.6819 (mm-30) REVERT: C 490 ASP cc_start: 0.8448 (t0) cc_final: 0.7894 (t0) REVERT: C 572 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7847 (pt0) REVERT: D 125 GLU cc_start: 0.7632 (tp30) cc_final: 0.6813 (mm-30) REVERT: D 490 ASP cc_start: 0.8447 (t0) cc_final: 0.7865 (t0) REVERT: D 572 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7862 (pt0) outliers start: 58 outliers final: 10 residues processed: 262 average time/residue: 0.8077 time to fit residues: 236.3209 Evaluate side-chains 224 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 270 VAL 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 D residue 270 VAL Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 727 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 150 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125894 restraints weight = 23813.732| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.90 r_work: 0.3187 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24484 Z= 0.110 Angle : 0.535 13.366 33244 Z= 0.268 Chirality : 0.039 0.155 3724 Planarity : 0.004 0.089 4336 Dihedral : 7.209 101.217 3660 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % Rotamer: Outliers : 3.77 % Allowed : 18.76 % Favored : 77.47 % 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: 0.77 (0.15), residues: 3108 helix: 2.17 (0.14), residues: 1576 sheet: 0.52 (0.26), residues: 344 loop : -1.92 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 361 TYR 0.011 0.001 TYR B 491 PHE 0.010 0.001 PHE D 573 TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00227 (24484) covalent geometry : angle 0.53463 (33244) hydrogen bonds : bond 0.04467 ( 1168) hydrogen bonds : angle 3.86219 ( 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 319 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 229 time to evaluate : 0.844 Fit side-chains REVERT: A 125 GLU cc_start: 0.7772 (tp30) cc_final: 0.6816 (mm-30) REVERT: A 490 ASP cc_start: 0.8474 (t0) cc_final: 0.8109 (t0) REVERT: A 572 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7882 (pt0) REVERT: A 583 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 613 MET cc_start: 0.8386 (mtp) cc_final: 0.7991 (ttm) REVERT: A 725 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: B 125 GLU cc_start: 0.7790 (tp30) cc_final: 0.6825 (mm-30) REVERT: B 572 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7876 (pt0) REVERT: B 613 MET cc_start: 0.8402 (mtp) cc_final: 0.8011 (ttm) REVERT: C 125 GLU cc_start: 0.7811 (tp30) cc_final: 0.6858 (mm-30) REVERT: C 490 ASP cc_start: 0.8504 (t0) cc_final: 0.8166 (t0) REVERT: C 572 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7886 (pt0) REVERT: C 583 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: C 613 MET cc_start: 0.8396 (mtp) cc_final: 0.8007 (ttm) REVERT: D 125 GLU cc_start: 0.7806 (tp30) cc_final: 0.6850 (mm-30) REVERT: D 490 ASP cc_start: 0.8512 (t0) cc_final: 0.8186 (t0) REVERT: D 572 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7899 (pt0) REVERT: D 613 MET cc_start: 0.8409 (mtp) cc_final: 0.8018 (ttm) outliers start: 90 outliers final: 30 residues processed: 283 average time/residue: 0.7181 time to fit residues: 229.1583 Evaluate side-chains 248 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 583 GLU 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 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 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 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 408 CYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 6.9990 chunk 197 optimal weight: 0.0050 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.0070 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 263 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 288 optimal weight: 0.7980 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4081 r_free = 0.4081 target = 0.184717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129582 restraints weight = 23968.031| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.92 r_work: 0.3237 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24484 Z= 0.091 Angle : 0.504 13.281 33244 Z= 0.250 Chirality : 0.038 0.144 3724 Planarity : 0.003 0.071 4336 Dihedral : 6.967 104.290 3655 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.76 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 20.23 % Favored : 77.60 % 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: 0.96 (0.15), residues: 3108 helix: 2.40 (0.14), residues: 1568 sheet: 0.56 (0.27), residues: 344 loop : -1.90 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 723 TYR 0.007 0.001 TYR D 720 PHE 0.004 0.001 PHE D 555 TRP 0.006 0.001 TRP C 395 HIS 0.002 0.000 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00179 (24484) covalent geometry : angle 0.50357 (33244) hydrogen bonds : bond 0.03299 ( 1168) hydrogen bonds : angle 3.71610 ( 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 270 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.892 Fit side-chains REVERT: A 125 GLU cc_start: 0.7792 (tp30) cc_final: 0.6795 (mm-30) REVERT: A 490 ASP cc_start: 0.8327 (t0) cc_final: 0.7910 (t70) REVERT: A 572 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7874 (pt0) REVERT: A 613 MET cc_start: 0.8339 (mtp) cc_final: 0.7935 (ttm) REVERT: B 125 GLU cc_start: 0.7787 (tp30) cc_final: 0.6784 (mm-30) REVERT: B 490 ASP cc_start: 0.8432 (t0) cc_final: 0.8048 (t70) REVERT: B 572 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7867 (pt0) REVERT: B 613 MET cc_start: 0.8342 (mtp) cc_final: 0.7940 (ttm) REVERT: C 125 GLU cc_start: 0.7805 (tp30) cc_final: 0.6817 (mm-30) REVERT: C 303 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6759 (tt0) REVERT: C 490 ASP cc_start: 0.8348 (t0) cc_final: 0.7923 (t70) REVERT: C 572 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7882 (pt0) REVERT: C 613 MET cc_start: 0.8347 (mtp) cc_final: 0.7947 (ttm) REVERT: D 125 GLU cc_start: 0.7808 (tp30) cc_final: 0.6810 (mm-30) REVERT: D 303 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6774 (tt0) REVERT: D 359 ARG cc_start: 0.6010 (mtm-85) cc_final: 0.5756 (mtm-85) REVERT: D 490 ASP cc_start: 0.8353 (t0) cc_final: 0.7934 (t70) REVERT: D 530 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8409 (mp) REVERT: D 572 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7892 (pt0) REVERT: D 613 MET cc_start: 0.8353 (mtp) cc_final: 0.7954 (ttm) outliers start: 52 outliers final: 29 residues processed: 249 average time/residue: 0.7293 time to fit residues: 204.9822 Evaluate side-chains 245 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 270 VAL 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 729 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 530 LEU 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 778 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 226 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 125 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS B 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 655 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121328 restraints weight = 23398.231| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.93 r_work: 0.3110 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24484 Z= 0.177 Angle : 0.640 13.552 33244 Z= 0.322 Chirality : 0.043 0.168 3724 Planarity : 0.005 0.067 4336 Dihedral : 7.140 94.471 3650 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.54 % Favored : 95.05 % Rotamer: Outliers : 4.19 % Allowed : 18.43 % Favored : 77.39 % 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: 0.60 (0.15), residues: 3108 helix: 2.10 (0.13), residues: 1568 sheet: 0.40 (0.27), residues: 344 loop : -2.06 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 723 TYR 0.016 0.002 TYR D 491 PHE 0.010 0.002 PHE B 218 TRP 0.010 0.001 TRP B 395 HIS 0.006 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00412 (24484) covalent geometry : angle 0.63975 (33244) hydrogen bonds : bond 0.06467 ( 1168) hydrogen bonds : angle 3.93919 ( 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 298 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 198 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7826 (tp30) cc_final: 0.6788 (mm-30) REVERT: A 149 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7283 (t0) REVERT: A 583 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: A 611 ARG cc_start: 0.7061 (mmp-170) cc_final: 0.6848 (mmp-170) REVERT: A 613 MET cc_start: 0.8491 (mtp) cc_final: 0.7960 (ttm) REVERT: A 762 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6575 (mtp85) REVERT: B 125 GLU cc_start: 0.7831 (tp30) cc_final: 0.6778 (mm-30) REVERT: B 149 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7287 (t0) REVERT: B 611 ARG cc_start: 0.7071 (mmp-170) cc_final: 0.6855 (mmp-170) REVERT: B 613 MET cc_start: 0.8492 (mtp) cc_final: 0.7969 (ttm) REVERT: B 762 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6531 (mtp85) REVERT: C 125 GLU cc_start: 0.7823 (tp30) cc_final: 0.6793 (mm-30) REVERT: C 149 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7273 (t0) REVERT: C 583 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: C 611 ARG cc_start: 0.7073 (mmp-170) cc_final: 0.6860 (mmp-170) REVERT: C 613 MET cc_start: 0.8487 (mtp) cc_final: 0.7957 (ttm) REVERT: C 762 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6539 (mtp85) REVERT: D 125 GLU cc_start: 0.7821 (tp30) cc_final: 0.6793 (mm-30) REVERT: D 149 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7266 (t0) REVERT: D 359 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5844 (mtm-85) REVERT: D 611 ARG cc_start: 0.7082 (mmp-170) cc_final: 0.6865 (mmp-170) REVERT: D 613 MET cc_start: 0.8502 (mtp) cc_final: 0.7981 (ttm) REVERT: D 762 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6545 (mtp85) outliers start: 100 outliers final: 39 residues processed: 269 average time/residue: 0.6966 time to fit residues: 212.7468 Evaluate side-chains 234 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 201 ASP Chi-restraints excluded: chain A residue 203 ASP 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 583 GLU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 726 VAL 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 149 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 203 ASP 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 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 149 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 203 ASP 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 583 GLU 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 149 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 203 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 596 SER 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 762 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS B 655 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 655 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121504 restraints weight = 23589.867| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.97 r_work: 0.3110 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24484 Z= 0.173 Angle : 0.632 13.490 33244 Z= 0.318 Chirality : 0.043 0.157 3724 Planarity : 0.005 0.064 4336 Dihedral : 7.140 96.609 3649 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Rotamer: Outliers : 3.60 % Allowed : 19.56 % Favored : 76.84 % 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: 0.45 (0.15), residues: 3108 helix: 1.89 (0.13), residues: 1584 sheet: 0.32 (0.27), residues: 344 loop : -2.05 (0.15), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 723 TYR 0.015 0.002 TYR A 491 PHE 0.010 0.001 PHE D 573 TRP 0.010 0.001 TRP C 395 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00402 (24484) covalent geometry : angle 0.63200 (33244) hydrogen bonds : bond 0.06152 ( 1168) hydrogen bonds : angle 3.93824 ( 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 288 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 202 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7804 (tp30) cc_final: 0.6730 (mm-30) REVERT: A 149 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7281 (t0) REVERT: A 583 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 611 ARG cc_start: 0.7113 (mmp-170) cc_final: 0.6901 (mmp-170) REVERT: A 613 MET cc_start: 0.8539 (mtp) cc_final: 0.7997 (ttm) REVERT: A 727 ARG cc_start: 0.0669 (OUTLIER) cc_final: -0.0047 (ttp80) REVERT: B 125 GLU cc_start: 0.7816 (tp30) cc_final: 0.6723 (mm-30) REVERT: B 149 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7272 (t0) REVERT: B 611 ARG cc_start: 0.7118 (mmp-170) cc_final: 0.6905 (mmp-170) REVERT: B 613 MET cc_start: 0.8540 (mtp) cc_final: 0.8044 (ttm) REVERT: C 125 GLU cc_start: 0.7807 (tp30) cc_final: 0.6739 (mm-30) REVERT: C 149 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7260 (t0) REVERT: C 583 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: C 611 ARG cc_start: 0.7112 (mmp-170) cc_final: 0.6898 (mmp-170) REVERT: C 613 MET cc_start: 0.8532 (mtp) cc_final: 0.7994 (ttm) REVERT: D 125 GLU cc_start: 0.7797 (tp30) cc_final: 0.6739 (mm-30) REVERT: D 149 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7263 (t0) REVERT: D 359 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5814 (mtm-85) REVERT: D 611 ARG cc_start: 0.7126 (mmp-170) cc_final: 0.6911 (mmp-170) REVERT: D 613 MET cc_start: 0.8550 (mtp) cc_final: 0.8055 (ttm) outliers start: 86 outliers final: 44 residues processed: 270 average time/residue: 0.6716 time to fit residues: 205.6518 Evaluate side-chains 245 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 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 583 GLU Chi-restraints excluded: chain A residue 596 SER 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 B residue 149 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 335 LEU Chi-restraints excluded: chain B residue 347 SER 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 C residue 149 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 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 583 GLU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain D residue 149 ASP 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 354 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 725 GLU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 727 ARG Chi-restraints excluded: chain D residue 729 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 163 optimal weight: 0.0870 chunk 184 optimal weight: 0.7980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 655 GLN B 318 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 655 GLN D 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126373 restraints weight = 23636.179| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.96 r_work: 0.3187 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24484 Z= 0.104 Angle : 0.521 13.325 33244 Z= 0.263 Chirality : 0.039 0.143 3724 Planarity : 0.004 0.049 4336 Dihedral : 6.951 102.797 3649 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.83 % Favored : 94.76 % Rotamer: Outliers : 2.72 % Allowed : 20.52 % Favored : 76.76 % 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: 2.20 (0.13), residues: 1580 sheet: 0.35 (0.27), residues: 344 loop : -1.95 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 361 TYR 0.009 0.001 TYR A 720 PHE 0.011 0.001 PHE A 573 TRP 0.009 0.001 TRP B 395 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00209 (24484) covalent geometry : angle 0.52060 (33244) hydrogen bonds : bond 0.03874 ( 1168) hydrogen bonds : angle 3.76819 ( 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 270 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7808 (tp30) cc_final: 0.6811 (mm-30) REVERT: A 490 ASP cc_start: 0.8440 (t0) cc_final: 0.7865 (t0) REVERT: A 611 ARG cc_start: 0.6963 (mmp-170) cc_final: 0.6750 (mmp-170) REVERT: A 613 MET cc_start: 0.8440 (mtp) cc_final: 0.7985 (ttm) REVERT: A 727 ARG cc_start: 0.0526 (OUTLIER) cc_final: -0.0133 (ttp80) REVERT: B 125 GLU cc_start: 0.7807 (tp30) cc_final: 0.6804 (mm-30) REVERT: B 490 ASP cc_start: 0.8469 (t0) cc_final: 0.7808 (t0) REVERT: B 572 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7918 (pt0) REVERT: B 611 ARG cc_start: 0.6976 (mmp-170) cc_final: 0.6763 (mmp-170) REVERT: B 613 MET cc_start: 0.8430 (mtp) cc_final: 0.7996 (ttm) REVERT: C 125 GLU cc_start: 0.7807 (tp30) cc_final: 0.6815 (mm-30) REVERT: C 490 ASP cc_start: 0.8445 (t0) cc_final: 0.7858 (t0) REVERT: C 611 ARG cc_start: 0.6970 (mmp-170) cc_final: 0.6759 (mmp-170) REVERT: C 613 MET cc_start: 0.8437 (mtp) cc_final: 0.7985 (ttm) REVERT: D 125 GLU cc_start: 0.7802 (tp30) cc_final: 0.6801 (mm-30) REVERT: D 359 ARG cc_start: 0.5989 (mtm-85) cc_final: 0.5730 (mtm-85) REVERT: D 490 ASP cc_start: 0.8471 (t0) cc_final: 0.7893 (t0) REVERT: D 611 ARG cc_start: 0.6971 (mmp-170) cc_final: 0.6755 (mmp-170) REVERT: D 613 MET cc_start: 0.8438 (mtp) cc_final: 0.8006 (ttm) outliers start: 65 outliers final: 33 residues processed: 254 average time/residue: 0.7171 time to fit residues: 205.3534 Evaluate side-chains 231 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 726 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 729 THR 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 726 VAL 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 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 354 LEU 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 725 GLU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 727 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 43 optimal weight: 0.0980 chunk 162 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 651 HIS D 655 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122611 restraints weight = 23495.741| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.93 r_work: 0.3131 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24484 Z= 0.143 Angle : 0.577 13.349 33244 Z= 0.292 Chirality : 0.041 0.145 3724 Planarity : 0.004 0.048 4336 Dihedral : 7.009 97.251 3649 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.15 % Favored : 94.43 % Rotamer: Outliers : 2.97 % Allowed : 20.81 % Favored : 76.21 % 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: 0.65 (0.15), residues: 3108 helix: 2.10 (0.13), residues: 1580 sheet: 0.35 (0.27), residues: 344 loop : -1.99 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 762 TYR 0.013 0.001 TYR D 491 PHE 0.008 0.001 PHE D 573 TRP 0.009 0.001 TRP A 395 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00323 (24484) covalent geometry : angle 0.57693 (33244) hydrogen bonds : bond 0.05386 ( 1168) hydrogen bonds : angle 3.83393 ( 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 268 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 197 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6230 (tppt) REVERT: A 125 GLU cc_start: 0.7836 (tp30) cc_final: 0.6827 (mm-30) REVERT: A 583 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 611 ARG cc_start: 0.6983 (mmp-170) cc_final: 0.6767 (mmp-170) REVERT: A 613 MET cc_start: 0.8454 (mtp) cc_final: 0.7961 (ttm) REVERT: A 727 ARG cc_start: 0.0493 (OUTLIER) cc_final: -0.0173 (ttp80) REVERT: B 21 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6161 (tppt) REVERT: B 125 GLU cc_start: 0.7833 (tp30) cc_final: 0.6804 (mm-30) REVERT: B 611 ARG cc_start: 0.6989 (mmp-170) cc_final: 0.6771 (mmp-170) REVERT: B 613 MET cc_start: 0.8456 (mtp) cc_final: 0.7956 (ttm) REVERT: C 21 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6259 (tppt) REVERT: C 125 GLU cc_start: 0.7824 (tp30) cc_final: 0.6822 (mm-30) REVERT: C 583 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: C 611 ARG cc_start: 0.6983 (mmp-170) cc_final: 0.6768 (mmp-170) REVERT: C 613 MET cc_start: 0.8451 (mtp) cc_final: 0.7961 (ttm) REVERT: D 21 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6194 (tppt) REVERT: D 125 GLU cc_start: 0.7813 (tp30) cc_final: 0.6818 (mm-30) REVERT: D 359 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5803 (mtm-85) REVERT: D 611 ARG cc_start: 0.6989 (mmp-170) cc_final: 0.6767 (mmp-170) REVERT: D 613 MET cc_start: 0.8469 (mtp) cc_final: 0.7966 (ttm) outliers start: 71 outliers final: 40 residues processed: 255 average time/residue: 0.7157 time to fit residues: 206.2861 Evaluate side-chains 245 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS 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 354 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 596 SER 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 778 VAL Chi-restraints excluded: chain B residue 21 LYS 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 596 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain C residue 21 LYS 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 583 GLU Chi-restraints excluded: chain C residue 596 SER 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 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 725 GLU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 778 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 305 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 651 HIS D 655 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122705 restraints weight = 23667.792| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.91 r_work: 0.3115 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24484 Z= 0.155 Angle : 0.595 13.339 33244 Z= 0.301 Chirality : 0.042 0.146 3724 Planarity : 0.004 0.048 4336 Dihedral : 7.067 96.774 3649 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.92 % Favored : 94.79 % Rotamer: Outliers : 2.85 % Allowed : 21.19 % 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: 0.53 (0.15), residues: 3108 helix: 1.99 (0.13), residues: 1580 sheet: 0.30 (0.27), residues: 344 loop : -2.04 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 762 TYR 0.017 0.002 TYR D 491 PHE 0.010 0.001 PHE C 573 TRP 0.010 0.001 TRP A 395 HIS 0.005 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00353 (24484) covalent geometry : angle 0.59461 (33244) hydrogen bonds : bond 0.05674 ( 1168) hydrogen bonds : angle 3.87948 ( 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 264 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 196 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6213 (tppt) REVERT: A 125 GLU cc_start: 0.7822 (tp30) cc_final: 0.6778 (mm-30) REVERT: A 583 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 611 ARG cc_start: 0.7028 (mmp-170) cc_final: 0.6813 (mmp-170) REVERT: A 613 MET cc_start: 0.8467 (mtp) cc_final: 0.7986 (ttm) REVERT: A 727 ARG cc_start: 0.0527 (OUTLIER) cc_final: -0.0163 (ttp80) REVERT: B 21 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6173 (tppt) REVERT: B 125 GLU cc_start: 0.7824 (tp30) cc_final: 0.6766 (mm-30) REVERT: B 611 ARG cc_start: 0.7030 (mmp-170) cc_final: 0.6810 (mmp-170) REVERT: B 613 MET cc_start: 0.8463 (mtp) cc_final: 0.7969 (ttm) REVERT: C 21 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6192 (tppt) REVERT: C 125 GLU cc_start: 0.7813 (tp30) cc_final: 0.6784 (mm-30) REVERT: C 583 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: C 611 ARG cc_start: 0.7029 (mmp-170) cc_final: 0.6812 (mmp-170) REVERT: C 613 MET cc_start: 0.8473 (mtp) cc_final: 0.8001 (ttm) REVERT: D 21 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6210 (tppt) REVERT: D 125 GLU cc_start: 0.7808 (tp30) cc_final: 0.6785 (mm-30) REVERT: D 359 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5816 (mtm-85) REVERT: D 611 ARG cc_start: 0.7032 (mmp-170) cc_final: 0.6812 (mmp-170) REVERT: D 613 MET cc_start: 0.8477 (mtp) cc_final: 0.7982 (ttm) outliers start: 68 outliers final: 46 residues processed: 255 average time/residue: 0.7280 time to fit residues: 209.7535 Evaluate side-chains 246 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS 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 354 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 583 GLU 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 726 VAL 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 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 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 B residue 778 VAL Chi-restraints excluded: chain C residue 21 LYS 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 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 583 GLU 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 778 VAL Chi-restraints excluded: chain D residue 21 LYS 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 725 GLU Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 729 THR 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 200 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.4053 r_free = 0.4053 target = 0.181889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126202 restraints weight = 23662.441| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.97 r_work: 0.3188 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24484 Z= 0.102 Angle : 0.514 13.128 33244 Z= 0.260 Chirality : 0.039 0.140 3724 Planarity : 0.004 0.042 4336 Dihedral : 6.869 102.169 3649 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.63 % Favored : 95.01 % Rotamer: Outliers : 2.55 % Allowed : 21.36 % Favored : 76.09 % 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: 0.78 (0.15), residues: 3108 helix: 2.23 (0.13), residues: 1580 sheet: 0.36 (0.27), residues: 344 loop : -1.95 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 762 TYR 0.012 0.001 TYR D 491 PHE 0.010 0.001 PHE B 573 TRP 0.009 0.001 TRP A 395 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00205 (24484) covalent geometry : angle 0.51412 (33244) hydrogen bonds : bond 0.03827 ( 1168) hydrogen bonds : angle 3.74659 ( 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 263 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6306 (tppt) REVERT: A 125 GLU cc_start: 0.7767 (tp30) cc_final: 0.6804 (mm-30) REVERT: A 490 ASP cc_start: 0.8596 (t0) cc_final: 0.8357 (t0) REVERT: A 611 ARG cc_start: 0.6930 (mmp-170) cc_final: 0.6709 (mmp-170) REVERT: A 613 MET cc_start: 0.8421 (mtp) cc_final: 0.7915 (ttm) REVERT: B 125 GLU cc_start: 0.7769 (tp30) cc_final: 0.6827 (mm-30) REVERT: B 490 ASP cc_start: 0.8443 (t0) cc_final: 0.7760 (t0) REVERT: B 611 ARG cc_start: 0.6918 (mmp-170) cc_final: 0.6702 (mmp-170) REVERT: B 613 MET cc_start: 0.8405 (mtp) cc_final: 0.7944 (ttm) REVERT: C 21 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6279 (tppt) REVERT: C 125 GLU cc_start: 0.7760 (tp30) cc_final: 0.6802 (mm-30) REVERT: C 611 ARG cc_start: 0.6921 (mmp-170) cc_final: 0.6705 (mmp-170) REVERT: C 613 MET cc_start: 0.8399 (mtp) cc_final: 0.7905 (ttm) REVERT: D 125 GLU cc_start: 0.7761 (tp30) cc_final: 0.6804 (mm-30) REVERT: D 359 ARG cc_start: 0.6082 (mtm-85) cc_final: 0.5816 (mtm-85) REVERT: D 611 ARG cc_start: 0.6914 (mmp-170) cc_final: 0.6692 (mmp-170) REVERT: D 613 MET cc_start: 0.8410 (mtp) cc_final: 0.7949 (ttm) outliers start: 61 outliers final: 37 residues processed: 247 average time/residue: 0.6886 time to fit residues: 193.0938 Evaluate side-chains 235 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS 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 726 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 778 VAL 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 726 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain C residue 21 LYS 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 408 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 778 VAL 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 408 CYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 725 GLU 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: 3.9990 chunk 24 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.4047 r_free = 0.4047 target = 0.181260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125365 restraints weight = 23685.631| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.97 r_work: 0.3172 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24484 Z= 0.107 Angle : 0.521 13.049 33244 Z= 0.263 Chirality : 0.039 0.142 3724 Planarity : 0.004 0.039 4336 Dihedral : 6.809 99.669 3649 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.50 % Favored : 95.08 % Rotamer: Outliers : 1.97 % Allowed : 22.40 % Favored : 75.63 % 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: 0.84 (0.15), residues: 3108 helix: 2.27 (0.13), residues: 1580 sheet: 0.37 (0.27), residues: 344 loop : -1.91 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 361 TYR 0.012 0.001 TYR D 491 PHE 0.009 0.001 PHE A 573 TRP 0.009 0.001 TRP A 395 HIS 0.003 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00224 (24484) covalent geometry : angle 0.52050 (33244) hydrogen bonds : bond 0.04187 ( 1168) hydrogen bonds : angle 3.73254 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9205.97 seconds wall clock time: 156 minutes 50.12 seconds (9410.12 seconds total)