Starting phenix.real_space_refine on Fri Feb 6 06:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mpp_48498/02_2026/9mpp_48498.map" } resolution = 3.1 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 332 5.49 5 S 88 5.16 5 C 13564 2.51 5 N 4222 2.21 5 O 4879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23091 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 826 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 806 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 833 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 896 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "H" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3385 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "J" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3421 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "M" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3345 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 20, 'TRANS': 396} Chain breaks: 2 Chain: "N" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2778 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 23, 'TRANS': 322} Chain: "K" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2271 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 16, 'TRANS': 264} Chain breaks: 1 Chain: "L" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1570 Classifications: {'peptide': 191} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 172} Chain breaks: 2 Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13254 SG CYS M 494 19.151 91.408 113.076 1.00300.00 S ATOM 13274 SG CYS M 497 21.507 92.392 109.702 1.00297.12 S ATOM 13396 SG CYS M 514 20.003 88.689 110.395 1.00110.39 S ATOM 13419 SG CYS M 517 22.745 90.011 111.903 1.00247.03 S ATOM 13587 SG CYS M 537 29.355 94.988 119.875 1.00189.03 S ATOM 13608 SG CYS M 540 28.445 94.733 115.693 1.00 80.68 S ATOM 13745 SG CYS M 559 30.092 97.531 117.287 1.00181.43 S ATOM 13767 SG CYS M 562 26.747 97.346 117.176 1.00101.94 S ATOM 13671 SG CYS M 549 33.647 95.642 131.750 1.00224.22 S ATOM 13705 SG CYS M 554 32.604 92.341 131.133 1.00156.55 S ATOM 13918 SG CYS M 583 30.509 95.396 129.907 1.00153.29 S ATOM 13944 SG CYS M 586 30.500 93.627 133.648 1.00193.47 S ATOM 16910 SG CYS N 96 36.576 33.121 76.769 1.00118.64 S ATOM 16930 SG CYS N 99 39.084 30.157 76.210 1.00223.45 S ATOM 17067 SG CYS N 118 36.969 30.508 73.665 1.00 85.54 S ATOM 17093 SG CYS N 121 35.906 28.675 76.272 1.00131.07 S ATOM 16992 SG CYS N 108 24.356 39.109 76.393 1.00166.92 S ATOM 17025 SG CYS N 113 25.128 38.722 79.959 1.00116.85 S ATOM 17241 SG CYS N 142 24.391 35.932 78.213 1.00212.22 S ATOM 17267 SG CYS N 145 21.284 38.040 79.357 1.00290.44 S ATOM 16575 SG CYS N 53 41.934 23.574 82.468 1.00242.09 S ATOM 16595 SG CYS N 56 44.902 24.019 79.632 1.00245.27 S ATOM 16722 SG CYS N 73 45.182 24.516 83.536 1.00257.26 S ATOM 16740 SG CYS N 76 44.396 27.147 81.574 1.00164.89 S Time building chain proxies: 4.59, per 1000 atoms: 0.20 Number of scatterers: 23091 At special positions: 0 Unit cell: (128.34, 129.168, 201.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 88 16.00 P 332 15.00 O 4879 8.00 N 4222 7.00 C 13564 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: 1.42 Conformation dependent library (CDL) restraints added in 837.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 514 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 517 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 497 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 494 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 559 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 540 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 562 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 537 " pdb=" ZN M1003 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 583 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 554 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 586 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 549 " pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 118 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 121 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 96 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 99 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 142 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 113 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 108 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 145 " pdb=" ZN N1003 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 56 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 73 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 53 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 76 " Number of angles added : 36 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 21 sheets defined 50.6% alpha, 7.2% beta 162 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.724A pdb=" N VAL A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.518A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.535A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.538A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.615A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.723A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.962A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.801A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.579A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.763A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.640A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.531A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.525A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.867A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.689A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.965A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.945A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.517A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.882A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 485 removed outlier: 3.568A pdb=" N GLU M 482 " --> pdb=" O ARG M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 489 through 493 removed outlier: 3.502A pdb=" N ILE M 493 " --> pdb=" O ILE M 490 " (cutoff:3.500A) Processing helix chain 'M' and resid 514 through 525 removed outlier: 3.608A pdb=" N ALA M 525 " --> pdb=" O PHE M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 560 through 567 Processing helix chain 'M' and resid 570 through 578 removed outlier: 3.531A pdb=" N GLU M 578 " --> pdb=" O ALA M 574 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 609 Processing helix chain 'M' and resid 627 through 631 Processing helix chain 'M' and resid 644 through 653 Processing helix chain 'M' and resid 666 through 677 removed outlier: 3.603A pdb=" N GLY M 673 " --> pdb=" O SER M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 686 through 690 Processing helix chain 'M' and resid 691 through 698 Processing helix chain 'M' and resid 729 through 742 removed outlier: 3.815A pdb=" N GLU M 733 " --> pdb=" O ARG M 729 " (cutoff:3.500A) Processing helix chain 'M' and resid 762 through 773 Processing helix chain 'M' and resid 783 through 785 No H-bonds generated for 'chain 'M' and resid 783 through 785' Processing helix chain 'M' and resid 860 through 868 Processing helix chain 'M' and resid 881 through 892 Processing helix chain 'M' and resid 894 through 903 Processing helix chain 'M' and resid 904 through 908 Processing helix chain 'N' and resid 39 through 44 removed outlier: 4.216A pdb=" N LYS N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'N' and resid 73 through 86 removed outlier: 3.507A pdb=" N PHE N 85 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 126 removed outlier: 3.632A pdb=" N VAL N 122 " --> pdb=" O CYS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 137 removed outlier: 3.814A pdb=" N MET N 137 " --> pdb=" O LYS N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 172 removed outlier: 4.028A pdb=" N GLN N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU N 171 " --> pdb=" O PHE N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 206 Processing helix chain 'N' and resid 228 through 235 Processing helix chain 'N' and resid 256 through 271 removed outlier: 3.817A pdb=" N LEU N 260 " --> pdb=" O PRO N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 302 Processing helix chain 'N' and resid 330 through 334 removed outlier: 3.797A pdb=" N HIS N 334 " --> pdb=" O ARG N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 354 removed outlier: 3.596A pdb=" N LEU N 343 " --> pdb=" O SER N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 366 removed outlier: 3.999A pdb=" N ASN N 366 " --> pdb=" O LYS N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 374 Proline residue: N 370 - end of helix removed outlier: 3.683A pdb=" N GLU N 373 " --> pdb=" O PRO N 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 631 Processing helix chain 'K' and resid 644 through 653 removed outlier: 3.543A pdb=" N LEU K 648 " --> pdb=" O ALA K 644 " (cutoff:3.500A) Processing helix chain 'K' and resid 666 through 678 removed outlier: 3.599A pdb=" N VAL K 672 " --> pdb=" O ASP K 668 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY K 673 " --> pdb=" O SER K 669 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET K 674 " --> pdb=" O ILE K 670 " (cutoff:3.500A) Processing helix chain 'K' and resid 686 through 690 Processing helix chain 'K' and resid 691 through 698 Processing helix chain 'K' and resid 727 through 729 No H-bonds generated for 'chain 'K' and resid 727 through 729' Processing helix chain 'K' and resid 730 through 742 removed outlier: 3.920A pdb=" N PHE K 734 " --> pdb=" O LEU K 730 " (cutoff:3.500A) Processing helix chain 'K' and resid 762 through 773 Processing helix chain 'K' and resid 782 through 787 Processing helix chain 'K' and resid 814 through 819 Processing helix chain 'K' and resid 860 through 869 Processing helix chain 'K' and resid 881 through 892 Processing helix chain 'K' and resid 894 through 903 Processing helix chain 'K' and resid 904 through 908 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'L' and resid 199 through 206 Processing helix chain 'L' and resid 228 through 235 Processing helix chain 'L' and resid 255 through 271 removed outlier: 4.265A pdb=" N TYR L 259 " --> pdb=" O PRO L 255 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU L 260 " --> pdb=" O PRO L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 302 Processing helix chain 'L' and resid 339 through 353 Processing helix chain 'L' and resid 365 through 374 removed outlier: 3.568A pdb=" N PHE L 368 " --> pdb=" O LYS L 365 " (cutoff:3.500A) Proline residue: L 370 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.799A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.125A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.277A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.018A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 504 through 505 Processing sheet with id=AB2, first strand: chain 'M' and resid 546 through 548 Processing sheet with id=AB3, first strand: chain 'M' and resid 591 through 592 Processing sheet with id=AB4, first strand: chain 'M' and resid 681 through 683 removed outlier: 6.370A pdb=" N ILE M 634 " --> pdb=" O VAL M 657 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG M 659 " --> pdb=" O ILE M 634 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL M 636 " --> pdb=" O ARG M 659 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY M 707 " --> pdb=" O LEU M 639 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 788 through 789 Processing sheet with id=AB6, first strand: chain 'M' and resid 823 through 825 Processing sheet with id=AB7, first strand: chain 'N' and resid 63 through 64 removed outlier: 3.513A pdb=" N THR N 63 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 218 through 221 removed outlier: 7.113A pdb=" N VAL N 192 " --> pdb=" O LYS N 219 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL N 221 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER N 194 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA N 244 " --> pdb=" O LEU N 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET N 283 " --> pdb=" O VAL N 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 682 through 683 removed outlier: 7.591A pdb=" N ILE K 634 " --> pdb=" O ASP K 658 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR K 660 " --> pdb=" O ILE K 634 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL K 636 " --> pdb=" O TYR K 660 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA K 662 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER K 638 " --> pdb=" O ALA K 662 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 788 through 789 Processing sheet with id=AC2, first strand: chain 'K' and resid 823 through 825 Processing sheet with id=AC3, first strand: chain 'L' and resid 218 through 220 removed outlier: 7.748A pdb=" N VAL L 192 " --> pdb=" O LYS L 219 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU L 193 " --> pdb=" O TYR L 242 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA L 244 " --> pdb=" O LEU L 193 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL L 241 " --> pdb=" O MET L 283 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL L 285 " --> pdb=" O VAL L 241 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY L 243 " --> pdb=" O VAL L 285 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 422 hydrogen bonds 844 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5785 1.34 - 1.46: 5879 1.46 - 1.58: 11807 1.58 - 1.70: 662 1.70 - 1.82: 127 Bond restraints: 24260 Sorted by residual: bond pdb=" N VAL L 222 " pdb=" CA VAL L 222 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 8.84e+00 bond pdb=" C2 SAH K1001 " pdb=" N3 SAH K1001 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" C2 SAH M1004 " pdb=" N3 SAH M1004 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" N ILE L 199 " pdb=" CA ILE L 199 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.04e-02 9.25e+03 8.23e+00 bond pdb=" N VAL M 877 " pdb=" CA VAL M 877 " ideal model delta sigma weight residual 1.458 1.484 -0.026 9.00e-03 1.23e+04 8.21e+00 ... (remaining 24255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 31687 2.10 - 4.20: 2432 4.20 - 6.29: 91 6.29 - 8.39: 3 8.39 - 10.49: 7 Bond angle restraints: 34220 Sorted by residual: angle pdb=" C4' DG I 104 " pdb=" C3' DG I 104 " pdb=" O3' DG I 104 " ideal model delta sigma weight residual 110.00 116.60 -6.60 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C ASN K 802 " pdb=" N ARG K 803 " pdb=" CA ARG K 803 " ideal model delta sigma weight residual 120.51 126.14 -5.63 1.45e+00 4.76e-01 1.51e+01 angle pdb=" C MET K 761 " pdb=" N GLY K 762 " pdb=" CA GLY K 762 " ideal model delta sigma weight residual 120.10 123.76 -3.66 9.50e-01 1.11e+00 1.49e+01 angle pdb=" O3' DC I 163 " pdb=" C3' DC I 163 " pdb=" C2' DC I 163 " ideal model delta sigma weight residual 111.50 105.81 5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" C ILE L 330 " pdb=" N ARG L 331 " pdb=" CA ARG L 331 " ideal model delta sigma weight residual 120.31 126.06 -5.75 1.52e+00 4.33e-01 1.43e+01 ... (remaining 34215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 11987 35.95 - 71.90: 1651 71.90 - 107.85: 32 107.85 - 143.80: 0 143.80 - 179.75: 4 Dihedral angle restraints: 13674 sinusoidal: 7810 harmonic: 5864 Sorted by residual: dihedral pdb=" CA GLU M 523 " pdb=" C GLU M 523 " pdb=" N CYS M 524 " pdb=" CA CYS M 524 " ideal model delta harmonic sigma weight residual -180.00 -150.21 -29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA PRO M 627 " pdb=" C PRO M 627 " pdb=" N ALA M 628 " pdb=" CA ALA M 628 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLY B 28 " pdb=" C GLY B 28 " pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 13671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2639 0.060 - 0.120: 993 0.120 - 0.180: 141 0.180 - 0.241: 12 0.241 - 0.301: 2 Chirality restraints: 3787 Sorted by residual: chirality pdb=" C3' DC I 10 " pdb=" C4' DC I 10 " pdb=" O3' DC I 10 " pdb=" C2' DC I 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' DG I 104 " pdb=" C4' DG I 104 " pdb=" O3' DG I 104 " pdb=" C2' DG I 104 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' DG I 138 " pdb=" C4' DG I 138 " pdb=" O3' DG I 138 " pdb=" C2' DG I 138 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3784 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 683 " 0.024 2.00e-02 2.50e+03 1.66e-02 5.54e+00 pdb=" CG TYR K 683 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR K 683 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR K 683 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR K 683 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR K 683 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR K 683 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 683 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 161 " 0.019 2.00e-02 2.50e+03 1.02e-02 3.10e+00 pdb=" N9 DG J 161 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG J 161 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 161 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 161 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 161 " 0.007 2.00e-02 2.50e+03 pdb=" O6 DG J 161 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DG J 161 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG J 161 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J 161 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 161 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG J 161 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " 0.022 2.00e-02 2.50e+03 9.87e-03 2.92e+00 pdb=" N9 DG I 131 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " -0.002 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2819 2.78 - 3.31: 20778 3.31 - 3.84: 41272 3.84 - 4.37: 50856 4.37 - 4.90: 74331 Nonbonded interactions: 190056 Sorted by model distance: nonbonded pdb=" OH TYR N 87 " pdb=" O ASN N 366 " model vdw 2.248 3.040 nonbonded pdb=" O ILE M 643 " pdb=" OH TYR M 874 " model vdw 2.330 3.040 nonbonded pdb=" CE1 PHE N 85 " pdb=" CD1 LEU N 176 " model vdw 2.331 3.760 nonbonded pdb=" O ARG K 635 " pdb=" N ASP K 702 " model vdw 2.333 3.120 nonbonded pdb=" OG1 THR N 63 " pdb=" NH2 ARG N 170 " model vdw 2.334 3.120 ... (remaining 190051 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 'A' selection = (chain 'E' and resid 36 through 135) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 113) } ncs_group { reference = (chain 'D' and resid 24 through 122) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.009 0.080 24284 Z= 0.604 Angle : 1.244 33.051 34256 Z= 0.827 Chirality : 0.060 0.301 3787 Planarity : 0.004 0.034 3212 Dihedral : 23.146 179.755 9884 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.06 % Allowed : 1.48 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -2.29 (0.16), residues: 1987 helix: -1.37 (0.14), residues: 945 sheet: -1.25 (0.42), residues: 136 loop : -1.61 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 823 TYR 0.040 0.002 TYR K 683 PHE 0.023 0.003 PHE M 851 TRP 0.023 0.002 TRP N 282 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00839 (24260) covalent geometry : angle 1.14395 (34220) hydrogen bonds : bond 0.13486 ( 1135) hydrogen bonds : angle 6.08509 ( 2872) metal coordination : bond 0.05623 ( 24) metal coordination : angle 15.10917 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7856 (mt) cc_final: 0.7641 (mp) REVERT: B 82 THR cc_start: 0.8909 (p) cc_final: 0.8701 (p) REVERT: C 36 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8734 (ttpt) REVERT: E 129 ARG cc_start: 0.8263 (tpt90) cc_final: 0.7936 (tpt90) REVERT: M 548 MET cc_start: 0.3387 (mtm) cc_final: 0.2968 (mtm) REVERT: M 781 ASP cc_start: 0.7721 (t0) cc_final: 0.7464 (t0) REVERT: M 820 GLU cc_start: 0.4109 (tp30) cc_final: 0.3830 (tp30) REVERT: M 848 PHE cc_start: 0.6538 (m-80) cc_final: 0.6336 (m-80) REVERT: N 340 GLU cc_start: 0.8746 (tp30) cc_final: 0.8544 (tp30) REVERT: K 775 SER cc_start: 0.7172 (p) cc_final: 0.6936 (m) REVERT: K 807 SER cc_start: 0.8685 (m) cc_final: 0.8335 (p) REVERT: K 855 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7596 (mmmt) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.2226 time to fit residues: 111.0351 Evaluate side-chains 304 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN A 108 ASN D 64 ASN D 79 HIS G 24 GLN H 79 HIS H 81 ASN M 873 HIS N 65 HIS N 110 ASN N 220 HIS N 264 HIS N 334 HIS K 694 HIS K 821 HIS K 873 HIS L 250 HIS L 313 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.199895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154586 restraints weight = 39993.408| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.65 r_work: 0.3749 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24284 Z= 0.246 Angle : 0.679 10.836 34256 Z= 0.373 Chirality : 0.040 0.153 3787 Planarity : 0.005 0.055 3212 Dihedral : 28.620 177.449 5847 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.48 % Allowed : 7.98 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.47 (0.18), residues: 1987 helix: 0.49 (0.16), residues: 949 sheet: -0.03 (0.49), residues: 120 loop : -1.18 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 882 TYR 0.024 0.002 TYR M 724 PHE 0.030 0.003 PHE M 902 TRP 0.012 0.002 TRP N 282 HIS 0.005 0.001 HIS M 677 Details of bonding type rmsd covalent geometry : bond 0.00548 (24260) covalent geometry : angle 0.65814 (34220) hydrogen bonds : bond 0.04684 ( 1135) hydrogen bonds : angle 3.92333 ( 2872) metal coordination : bond 0.01126 ( 24) metal coordination : angle 5.22452 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 321 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9085 (mt) cc_final: 0.8792 (mm) REVERT: A 129 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7659 (ttt180) REVERT: B 44 LYS cc_start: 0.8270 (tptt) cc_final: 0.7820 (tptp) REVERT: C 20 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8336 (ttp-170) REVERT: C 36 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8622 (ttpt) REVERT: C 77 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8116 (mtp-110) REVERT: C 84 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8341 (tp-100) REVERT: D 64 ASN cc_start: 0.8701 (m-40) cc_final: 0.8482 (m110) REVERT: E 109 LEU cc_start: 0.8996 (mt) cc_final: 0.8585 (mt) REVERT: E 129 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7749 (tpt90) REVERT: G 73 ASN cc_start: 0.8473 (t0) cc_final: 0.8021 (t0) REVERT: H 57 SER cc_start: 0.9026 (t) cc_final: 0.8739 (p) REVERT: M 675 VAL cc_start: 0.8418 (t) cc_final: 0.8167 (m) REVERT: M 742 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7580 (ttm-80) REVERT: N 51 ASP cc_start: 0.6409 (m-30) cc_final: 0.5785 (p0) REVERT: N 186 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7169 (mmt180) REVERT: N 202 GLU cc_start: 0.7289 (mp0) cc_final: 0.6890 (mp0) REVERT: N 239 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) REVERT: N 260 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6605 (tp) REVERT: N 340 GLU cc_start: 0.7395 (tp30) cc_final: 0.7180 (tp30) REVERT: N 342 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6921 (mm-30) REVERT: K 641 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7720 (t0) REVERT: K 829 LYS cc_start: 0.6718 (mptt) cc_final: 0.6474 (mmmm) REVERT: K 855 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6867 (mmmt) REVERT: K 864 MET cc_start: 0.7126 (ttm) cc_final: 0.6873 (ttm) REVERT: K 887 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7594 (ttp-110) REVERT: L 343 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7225 (mp) outliers start: 26 outliers final: 13 residues processed: 333 average time/residue: 0.2179 time to fit residues: 100.9634 Evaluate side-chains 322 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 306 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 641 ASP Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 116 CYS Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 761 MET Chi-restraints excluded: chain K residue 785 VAL Chi-restraints excluded: chain L residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 223 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 162 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS C 38 ASN D 44 GLN E 68 GLN G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN N 262 GLN K 694 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.201077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155805 restraints weight = 40475.596| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.01 r_work: 0.3753 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24284 Z= 0.166 Angle : 0.592 9.442 34256 Z= 0.330 Chirality : 0.037 0.136 3787 Planarity : 0.004 0.036 3212 Dihedral : 28.316 179.899 5847 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.77 % Allowed : 9.81 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.22 (0.19), residues: 1987 helix: 1.20 (0.17), residues: 963 sheet: -0.28 (0.45), residues: 134 loop : -0.95 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 866 TYR 0.020 0.001 TYR M 793 PHE 0.027 0.002 PHE K 751 TRP 0.010 0.001 TRP L 324 HIS 0.007 0.001 HIS K 694 Details of bonding type rmsd covalent geometry : bond 0.00361 (24260) covalent geometry : angle 0.57474 (34220) hydrogen bonds : bond 0.03732 ( 1135) hydrogen bonds : angle 3.54674 ( 2872) metal coordination : bond 0.00677 ( 24) metal coordination : angle 4.39459 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9120 (mt) cc_final: 0.8805 (mm) REVERT: A 52 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7665 (mtt90) REVERT: A 129 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7728 (ttt180) REVERT: C 20 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8371 (ttp-110) REVERT: C 36 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8620 (ttpt) REVERT: C 77 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8128 (mtp-110) REVERT: E 129 ARG cc_start: 0.8170 (tpt90) cc_final: 0.7741 (tpt90) REVERT: G 73 ASN cc_start: 0.8468 (t0) cc_final: 0.7983 (t0) REVERT: H 57 SER cc_start: 0.9005 (t) cc_final: 0.8494 (p) REVERT: H 61 SER cc_start: 0.8792 (p) cc_final: 0.8495 (m) REVERT: H 81 ASN cc_start: 0.8781 (m-40) cc_final: 0.8538 (m110) REVERT: M 604 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7724 (tpp80) REVERT: M 675 VAL cc_start: 0.8366 (t) cc_final: 0.8059 (m) REVERT: M 742 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7624 (ttm-80) REVERT: M 793 TYR cc_start: 0.7491 (m-80) cc_final: 0.7236 (m-80) REVERT: N 51 ASP cc_start: 0.6365 (m-30) cc_final: 0.5732 (p0) REVERT: N 202 GLU cc_start: 0.7253 (mp0) cc_final: 0.6658 (mp0) REVERT: N 260 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6661 (tp) REVERT: N 340 GLU cc_start: 0.7518 (tp30) cc_final: 0.7285 (tp30) REVERT: N 342 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6942 (mm-30) REVERT: N 371 LEU cc_start: 0.4390 (OUTLIER) cc_final: 0.3225 (tp) REVERT: K 641 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7647 (t0) REVERT: K 694 HIS cc_start: 0.7597 (m90) cc_final: 0.6987 (m90) REVERT: K 774 GLU cc_start: 0.7520 (mp0) cc_final: 0.7013 (mp0) REVERT: K 807 SER cc_start: 0.8898 (m) cc_final: 0.8247 (p) REVERT: K 829 LYS cc_start: 0.7084 (mptt) cc_final: 0.6754 (mmmm) REVERT: K 855 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7027 (mmmt) REVERT: K 866 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7653 (ttm110) REVERT: L 343 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7373 (mp) outliers start: 31 outliers final: 19 residues processed: 326 average time/residue: 0.2166 time to fit residues: 100.0370 Evaluate side-chains 329 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 565 LEU Chi-restraints excluded: chain M residue 725 GLU Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 872 VAL Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 116 CYS Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 299 SER Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 785 VAL Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 901 LEU Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 10 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 GLN M 900 HIS L 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.199683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154568 restraints weight = 40087.506| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.60 r_work: 0.3748 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24284 Z= 0.184 Angle : 0.591 10.861 34256 Z= 0.330 Chirality : 0.038 0.206 3787 Planarity : 0.005 0.059 3212 Dihedral : 28.270 179.069 5847 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.00 % Allowed : 9.86 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.52 (0.19), residues: 1987 helix: 1.46 (0.17), residues: 966 sheet: 0.09 (0.48), residues: 124 loop : -0.84 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 882 TYR 0.015 0.001 TYR H 34 PHE 0.023 0.002 PHE K 751 TRP 0.009 0.001 TRP L 324 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00408 (24260) covalent geometry : angle 0.57970 (34220) hydrogen bonds : bond 0.03750 ( 1135) hydrogen bonds : angle 3.48905 ( 2872) metal coordination : bond 0.00636 ( 24) metal coordination : angle 3.62447 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9119 (mt) cc_final: 0.8904 (mm) REVERT: A 52 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7654 (mtt90) REVERT: A 129 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7707 (ttt180) REVERT: C 36 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8616 (ttpt) REVERT: C 77 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8142 (mtp-110) REVERT: E 129 ARG cc_start: 0.8185 (tpt90) cc_final: 0.7753 (tpt90) REVERT: F 78 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8294 (mtp180) REVERT: F 84 MET cc_start: 0.8421 (mmm) cc_final: 0.7980 (mmm) REVERT: G 63 LEU cc_start: 0.8340 (mt) cc_final: 0.8062 (mt) REVERT: G 73 ASN cc_start: 0.8463 (t0) cc_final: 0.7991 (t0) REVERT: G 101 THR cc_start: 0.8561 (m) cc_final: 0.8360 (t) REVERT: H 57 SER cc_start: 0.9019 (t) cc_final: 0.8527 (p) REVERT: H 61 SER cc_start: 0.8792 (p) cc_final: 0.8549 (m) REVERT: M 604 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7710 (tpp80) REVERT: M 675 VAL cc_start: 0.8434 (t) cc_final: 0.8159 (m) REVERT: N 51 ASP cc_start: 0.6423 (m-30) cc_final: 0.5789 (p0) REVERT: N 260 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6730 (tp) REVERT: N 340 GLU cc_start: 0.7421 (tp30) cc_final: 0.7202 (tp30) REVERT: N 342 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6872 (mm-30) REVERT: N 371 LEU cc_start: 0.4527 (OUTLIER) cc_final: 0.3796 (tp) REVERT: K 694 HIS cc_start: 0.7611 (m90) cc_final: 0.7407 (m-70) REVERT: K 807 SER cc_start: 0.8894 (m) cc_final: 0.8246 (p) REVERT: K 855 LYS cc_start: 0.7388 (mmmt) cc_final: 0.7022 (mmmt) REVERT: L 343 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7214 (mp) outliers start: 35 outliers final: 18 residues processed: 315 average time/residue: 0.2158 time to fit residues: 96.3370 Evaluate side-chains 313 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 565 LEU Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 872 VAL Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 761 MET Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.0040 chunk 200 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS F 93 GLN G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN N 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.200960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156279 restraints weight = 40167.462| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.60 r_work: 0.3783 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24284 Z= 0.143 Angle : 0.564 9.521 34256 Z= 0.317 Chirality : 0.036 0.135 3787 Planarity : 0.004 0.046 3212 Dihedral : 28.164 179.582 5847 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.05 % Allowed : 10.95 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 (0.19), residues: 1987 helix: 1.67 (0.17), residues: 964 sheet: 0.14 (0.47), residues: 124 loop : -0.75 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 803 TYR 0.029 0.001 TYR K 660 PHE 0.017 0.001 PHE N 280 TRP 0.013 0.001 TRP K 795 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00310 (24260) covalent geometry : angle 0.55399 (34220) hydrogen bonds : bond 0.03396 ( 1135) hydrogen bonds : angle 3.36942 ( 2872) metal coordination : bond 0.00483 ( 24) metal coordination : angle 3.38964 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9087 (mt) cc_final: 0.8881 (mm) REVERT: A 52 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7649 (mtt90) REVERT: A 82 LEU cc_start: 0.7876 (mm) cc_final: 0.7636 (mt) REVERT: A 129 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7679 (ttt180) REVERT: C 36 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8546 (ttpt) REVERT: C 77 ARG cc_start: 0.8384 (mtm110) cc_final: 0.8123 (mtp-110) REVERT: E 73 GLU cc_start: 0.7914 (tt0) cc_final: 0.7613 (mm-30) REVERT: E 118 THR cc_start: 0.8711 (t) cc_final: 0.8488 (p) REVERT: E 129 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7750 (tpt90) REVERT: F 84 MET cc_start: 0.8407 (mmm) cc_final: 0.8040 (mmm) REVERT: G 36 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8417 (ttpt) REVERT: G 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8017 (t0) REVERT: H 57 SER cc_start: 0.9023 (t) cc_final: 0.8502 (p) REVERT: H 61 SER cc_start: 0.8778 (p) cc_final: 0.8501 (m) REVERT: H 81 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8478 (m110) REVERT: M 604 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7726 (tpp80) REVERT: M 675 VAL cc_start: 0.8409 (t) cc_final: 0.8112 (m) REVERT: M 779 MET cc_start: 0.7353 (tmm) cc_final: 0.6732 (tmm) REVERT: M 880 MET cc_start: 0.6955 (ptp) cc_final: 0.6610 (mtp) REVERT: N 51 ASP cc_start: 0.6435 (m-30) cc_final: 0.5850 (p0) REVERT: N 340 GLU cc_start: 0.7443 (tp30) cc_final: 0.7219 (tp30) REVERT: N 342 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6906 (mm-30) REVERT: N 371 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.3393 (tp) REVERT: K 638 SER cc_start: 0.6605 (t) cc_final: 0.6181 (p) REVERT: K 641 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7474 (t0) REVERT: K 694 HIS cc_start: 0.7654 (m90) cc_final: 0.7428 (m-70) REVERT: K 829 LYS cc_start: 0.7022 (mmmm) cc_final: 0.6618 (mtpt) REVERT: K 855 LYS cc_start: 0.7403 (mmmt) cc_final: 0.7057 (mmmt) outliers start: 36 outliers final: 20 residues processed: 315 average time/residue: 0.2192 time to fit residues: 97.0620 Evaluate side-chains 324 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 872 VAL Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 758 VAL Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 190 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 91 optimal weight: 80.0000 chunk 194 optimal weight: 0.0970 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.201499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157951 restraints weight = 40514.458| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.80 r_work: 0.3766 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24284 Z= 0.141 Angle : 0.561 11.571 34256 Z= 0.314 Chirality : 0.036 0.137 3787 Planarity : 0.004 0.035 3212 Dihedral : 28.105 179.830 5847 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.11 % Allowed : 11.29 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.92 (0.19), residues: 1987 helix: 1.83 (0.17), residues: 964 sheet: 0.21 (0.47), residues: 124 loop : -0.67 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 83 TYR 0.022 0.001 TYR K 660 PHE 0.014 0.001 PHE N 280 TRP 0.013 0.001 TRP K 795 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00309 (24260) covalent geometry : angle 0.55198 (34220) hydrogen bonds : bond 0.03352 ( 1135) hydrogen bonds : angle 3.34261 ( 2872) metal coordination : bond 0.00452 ( 24) metal coordination : angle 3.09245 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7712 (mtt90) REVERT: A 129 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7691 (ttt180) REVERT: C 36 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8564 (ttpt) REVERT: C 77 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8110 (mtp-110) REVERT: E 73 GLU cc_start: 0.7927 (tt0) cc_final: 0.7592 (mm-30) REVERT: E 129 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7800 (tpt90) REVERT: G 36 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8439 (ttpt) REVERT: G 63 LEU cc_start: 0.8298 (mt) cc_final: 0.8041 (mt) REVERT: G 73 ASN cc_start: 0.8490 (t0) cc_final: 0.8025 (t0) REVERT: H 57 SER cc_start: 0.9037 (t) cc_final: 0.8513 (p) REVERT: H 61 SER cc_start: 0.8780 (p) cc_final: 0.8512 (m) REVERT: M 565 LEU cc_start: 0.8682 (pp) cc_final: 0.8216 (tt) REVERT: M 604 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7712 (tpp80) REVERT: M 675 VAL cc_start: 0.8447 (t) cc_final: 0.8229 (m) REVERT: M 779 MET cc_start: 0.7404 (tmm) cc_final: 0.6780 (tmm) REVERT: N 51 ASP cc_start: 0.6443 (m-30) cc_final: 0.5757 (p0) REVERT: N 340 GLU cc_start: 0.7492 (tp30) cc_final: 0.7275 (tp30) REVERT: N 342 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6961 (mm-30) REVERT: N 371 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.3493 (tp) REVERT: K 641 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7520 (t0) REVERT: K 694 HIS cc_start: 0.7704 (m90) cc_final: 0.7457 (m-70) REVERT: K 729 ARG cc_start: 0.7144 (ptp-170) cc_final: 0.6675 (mtt-85) REVERT: K 829 LYS cc_start: 0.7102 (mmmm) cc_final: 0.6827 (mmtt) REVERT: K 855 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7117 (mmmt) outliers start: 37 outliers final: 29 residues processed: 321 average time/residue: 0.2261 time to fit residues: 102.1389 Evaluate side-chains 328 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 669 SER Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 776 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 872 VAL Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 330 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 758 VAL Chi-restraints excluded: chain K residue 761 MET Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 872 VAL Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 165 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN F 93 GLN H 81 ASN N 262 GLN N 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.198041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152961 restraints weight = 39988.551| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.98 r_work: 0.3706 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24284 Z= 0.228 Angle : 0.618 10.814 34256 Z= 0.343 Chirality : 0.039 0.143 3787 Planarity : 0.005 0.059 3212 Dihedral : 28.160 178.663 5847 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.68 % Allowed : 11.46 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.68 (0.19), residues: 1987 helix: 1.58 (0.17), residues: 970 sheet: 0.26 (0.47), residues: 118 loop : -0.79 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 882 TYR 0.039 0.002 TYR K 660 PHE 0.019 0.002 PHE N 368 TRP 0.017 0.002 TRP K 698 HIS 0.005 0.001 HIS N 264 Details of bonding type rmsd covalent geometry : bond 0.00512 (24260) covalent geometry : angle 0.60863 (34220) hydrogen bonds : bond 0.04084 ( 1135) hydrogen bonds : angle 3.51928 ( 2872) metal coordination : bond 0.00657 ( 24) metal coordination : angle 3.40254 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7742 (mtt90) REVERT: A 129 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7738 (ttt180) REVERT: C 36 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8566 (ttpt) REVERT: C 77 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8172 (mtp-110) REVERT: C 84 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8384 (tp-100) REVERT: D 43 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8420 (mmtt) REVERT: D 79 HIS cc_start: 0.7802 (m-70) cc_final: 0.7590 (m90) REVERT: E 129 ARG cc_start: 0.8237 (tpt90) cc_final: 0.7865 (tpt90) REVERT: F 84 MET cc_start: 0.8428 (mmm) cc_final: 0.8116 (mmm) REVERT: G 36 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8505 (ttpt) REVERT: G 73 ASN cc_start: 0.8533 (t0) cc_final: 0.8072 (t0) REVERT: H 57 SER cc_start: 0.9092 (t) cc_final: 0.8557 (p) REVERT: H 61 SER cc_start: 0.8813 (p) cc_final: 0.8592 (m) REVERT: H 81 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (m110) REVERT: M 565 LEU cc_start: 0.8711 (pp) cc_final: 0.8187 (tt) REVERT: M 604 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7706 (tpp80) REVERT: M 675 VAL cc_start: 0.8603 (t) cc_final: 0.8388 (m) REVERT: M 770 SER cc_start: 0.8526 (p) cc_final: 0.8305 (p) REVERT: M 771 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7520 (mmt90) REVERT: M 880 MET cc_start: 0.7401 (ptp) cc_final: 0.7091 (mtp) REVERT: N 51 ASP cc_start: 0.6657 (m-30) cc_final: 0.5850 (p0) REVERT: N 202 GLU cc_start: 0.7283 (mp0) cc_final: 0.7070 (mp0) REVERT: N 260 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6744 (tp) REVERT: N 323 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.5974 (p) REVERT: N 324 TRP cc_start: 0.7383 (m-90) cc_final: 0.6925 (m-90) REVERT: N 340 GLU cc_start: 0.7486 (tp30) cc_final: 0.7256 (tp30) REVERT: N 342 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7015 (mm-30) REVERT: N 371 LEU cc_start: 0.4894 (OUTLIER) cc_final: 0.3790 (tp) REVERT: K 641 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7046 (t70) REVERT: K 645 THR cc_start: 0.7011 (m) cc_final: 0.6807 (p) REVERT: K 694 HIS cc_start: 0.7698 (m90) cc_final: 0.7462 (m-70) REVERT: K 829 LYS cc_start: 0.7262 (mmmm) cc_final: 0.7020 (mmtt) REVERT: K 855 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7264 (mmmt) REVERT: K 880 MET cc_start: 0.7312 (mtm) cc_final: 0.7066 (mtm) REVERT: K 885 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6802 (ttt180) REVERT: K 907 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 47 outliers final: 31 residues processed: 318 average time/residue: 0.2075 time to fit residues: 92.6666 Evaluate side-chains 330 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 669 SER Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain M residue 771 ARG Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 776 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 872 VAL Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 758 VAL Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 862 THR Chi-restraints excluded: chain K residue 882 ARG Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 193 optimal weight: 3.9990 chunk 211 optimal weight: 50.0000 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 148 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.199295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154034 restraints weight = 39973.512| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.96 r_work: 0.3731 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24284 Z= 0.162 Angle : 0.587 10.661 34256 Z= 0.326 Chirality : 0.037 0.136 3787 Planarity : 0.004 0.062 3212 Dihedral : 28.078 179.862 5847 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.82 % Allowed : 12.54 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.82 (0.19), residues: 1987 helix: 1.71 (0.17), residues: 968 sheet: 0.25 (0.47), residues: 118 loop : -0.71 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 729 TYR 0.024 0.001 TYR K 660 PHE 0.017 0.001 PHE N 261 TRP 0.014 0.001 TRP K 860 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00358 (24260) covalent geometry : angle 0.57451 (34220) hydrogen bonds : bond 0.03595 ( 1135) hydrogen bonds : angle 3.38992 ( 2872) metal coordination : bond 0.01037 ( 24) metal coordination : angle 3.81652 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9008 (mm) cc_final: 0.8537 (mt) REVERT: A 52 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7703 (mtt90) REVERT: A 129 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7760 (ttt180) REVERT: C 36 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8566 (ttpt) REVERT: C 77 ARG cc_start: 0.8454 (mtm110) cc_final: 0.8181 (mtp-110) REVERT: D 43 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8398 (mmtt) REVERT: E 61 LEU cc_start: 0.7403 (mt) cc_final: 0.7177 (mp) REVERT: E 129 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7869 (tpt90) REVERT: F 84 MET cc_start: 0.8417 (mmm) cc_final: 0.8134 (mmm) REVERT: G 36 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8463 (ttpt) REVERT: G 73 ASN cc_start: 0.8534 (t0) cc_final: 0.8064 (t0) REVERT: H 57 SER cc_start: 0.9078 (t) cc_final: 0.8554 (p) REVERT: H 61 SER cc_start: 0.8809 (p) cc_final: 0.8587 (m) REVERT: M 515 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7624 (tm-30) REVERT: M 565 LEU cc_start: 0.8716 (pp) cc_final: 0.8180 (tt) REVERT: M 604 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7714 (tpp80) REVERT: M 671 THR cc_start: 0.7580 (m) cc_final: 0.7378 (p) REVERT: M 675 VAL cc_start: 0.8505 (t) cc_final: 0.8293 (m) REVERT: M 771 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7421 (mmt90) REVERT: M 880 MET cc_start: 0.7382 (ptp) cc_final: 0.7021 (mtp) REVERT: N 51 ASP cc_start: 0.6642 (m-30) cc_final: 0.5801 (p0) REVERT: N 323 VAL cc_start: 0.6289 (OUTLIER) cc_final: 0.5876 (p) REVERT: N 324 TRP cc_start: 0.7343 (m-90) cc_final: 0.6874 (m-90) REVERT: N 340 GLU cc_start: 0.7452 (tp30) cc_final: 0.7232 (tp30) REVERT: N 342 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6937 (mm-30) REVERT: N 371 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.3356 (tp) REVERT: K 641 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7563 (t70) REVERT: K 694 HIS cc_start: 0.7712 (m90) cc_final: 0.7471 (m-70) REVERT: K 829 LYS cc_start: 0.7144 (mmmm) cc_final: 0.6930 (mmtt) REVERT: K 855 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7269 (mmmt) REVERT: K 880 MET cc_start: 0.7290 (mtm) cc_final: 0.7046 (mtm) REVERT: K 885 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6797 (ttt180) REVERT: K 907 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7708 (mm-30) outliers start: 32 outliers final: 23 residues processed: 317 average time/residue: 0.2007 time to fit residues: 90.0128 Evaluate side-chains 327 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 669 SER Chi-restraints excluded: chain M residue 761 MET Chi-restraints excluded: chain M residue 771 ARG Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 776 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 727 THR Chi-restraints excluded: chain K residue 882 ARG Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN M 656 GLN ** K 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.198567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153082 restraints weight = 39871.951| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.98 r_work: 0.3718 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24284 Z= 0.182 Angle : 0.599 10.423 34256 Z= 0.332 Chirality : 0.038 0.138 3787 Planarity : 0.004 0.067 3212 Dihedral : 28.024 179.340 5847 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.94 % Allowed : 12.71 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 (0.19), residues: 1987 helix: 1.70 (0.17), residues: 967 sheet: 0.04 (0.45), residues: 128 loop : -0.74 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 882 TYR 0.026 0.001 TYR K 660 PHE 0.018 0.001 PHE N 368 TRP 0.011 0.001 TRP K 860 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00406 (24260) covalent geometry : angle 0.58786 (34220) hydrogen bonds : bond 0.03769 ( 1135) hydrogen bonds : angle 3.42117 ( 2872) metal coordination : bond 0.00707 ( 24) metal coordination : angle 3.55340 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9057 (mm) cc_final: 0.8624 (mt) REVERT: A 52 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7703 (mtt90) REVERT: A 129 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7735 (ttt180) REVERT: B 74 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 77 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8167 (mtp-110) REVERT: C 84 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8414 (tp-100) REVERT: D 43 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8387 (mmtt) REVERT: E 61 LEU cc_start: 0.7417 (mt) cc_final: 0.7176 (mp) REVERT: F 84 MET cc_start: 0.8404 (mmm) cc_final: 0.8114 (mmm) REVERT: G 36 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8442 (ttpt) REVERT: G 73 ASN cc_start: 0.8554 (t0) cc_final: 0.8077 (t0) REVERT: H 57 SER cc_start: 0.9058 (t) cc_final: 0.8521 (p) REVERT: M 515 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7686 (tm-30) REVERT: M 565 LEU cc_start: 0.8605 (pp) cc_final: 0.8035 (tt) REVERT: M 604 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7690 (tpp80) REVERT: M 771 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7520 (mmt90) REVERT: M 781 ASP cc_start: 0.7027 (t0) cc_final: 0.6658 (t0) REVERT: M 880 MET cc_start: 0.7408 (ptp) cc_final: 0.7118 (mtp) REVERT: N 51 ASP cc_start: 0.6686 (m-30) cc_final: 0.5810 (p0) REVERT: N 324 TRP cc_start: 0.7407 (m-90) cc_final: 0.6952 (m-90) REVERT: N 340 GLU cc_start: 0.7529 (tp30) cc_final: 0.7294 (tp30) REVERT: N 342 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7019 (mm-30) REVERT: N 371 LEU cc_start: 0.4906 (OUTLIER) cc_final: 0.3425 (tp) REVERT: K 643 ILE cc_start: 0.8829 (pt) cc_final: 0.8581 (pt) REVERT: K 694 HIS cc_start: 0.7782 (m90) cc_final: 0.7510 (m-70) REVERT: K 829 LYS cc_start: 0.7294 (mmmm) cc_final: 0.7069 (mmtt) REVERT: K 855 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7274 (mmmt) REVERT: K 880 MET cc_start: 0.7387 (mtm) cc_final: 0.7166 (mtm) REVERT: K 885 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6960 (ttt180) outliers start: 34 outliers final: 26 residues processed: 317 average time/residue: 0.2053 time to fit residues: 91.4863 Evaluate side-chains 329 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 669 SER Chi-restraints excluded: chain M residue 771 ARG Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 776 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 223 ASP Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 727 THR Chi-restraints excluded: chain K residue 852 MET Chi-restraints excluded: chain K residue 882 ARG Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 113 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 132 optimal weight: 0.0770 chunk 169 optimal weight: 0.6980 chunk 204 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN H 81 ASN ** K 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.198304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152658 restraints weight = 39839.246| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.86 r_work: 0.3725 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24284 Z= 0.181 Angle : 0.600 10.025 34256 Z= 0.333 Chirality : 0.038 0.140 3787 Planarity : 0.004 0.076 3212 Dihedral : 27.973 179.322 5847 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 13.51 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 (0.19), residues: 1987 helix: 1.69 (0.17), residues: 966 sheet: 0.10 (0.47), residues: 118 loop : -0.72 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 99 TYR 0.020 0.001 TYR K 660 PHE 0.046 0.002 PHE N 261 TRP 0.012 0.001 TRP K 795 HIS 0.010 0.001 HIS M 677 Details of bonding type rmsd covalent geometry : bond 0.00405 (24260) covalent geometry : angle 0.58969 (34220) hydrogen bonds : bond 0.03768 ( 1135) hydrogen bonds : angle 3.42636 ( 2872) metal coordination : bond 0.00671 ( 24) metal coordination : angle 3.42314 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9048 (mm) cc_final: 0.8654 (mt) REVERT: A 52 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7706 (mtt90) REVERT: A 129 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7761 (ttt180) REVERT: B 84 MET cc_start: 0.8335 (mmm) cc_final: 0.7970 (mmm) REVERT: C 77 ARG cc_start: 0.8470 (mtm110) cc_final: 0.8192 (mtp-110) REVERT: C 84 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8370 (tp-100) REVERT: D 43 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8387 (mmtt) REVERT: E 61 LEU cc_start: 0.7383 (mt) cc_final: 0.7153 (mp) REVERT: F 84 MET cc_start: 0.8404 (mmm) cc_final: 0.8190 (mmm) REVERT: G 36 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8436 (ttpt) REVERT: G 73 ASN cc_start: 0.8548 (t0) cc_final: 0.8088 (t0) REVERT: H 57 SER cc_start: 0.8981 (t) cc_final: 0.8604 (p) REVERT: M 565 LEU cc_start: 0.8595 (pp) cc_final: 0.7986 (tt) REVERT: M 604 ARG cc_start: 0.7982 (tpp80) cc_final: 0.7649 (tpp80) REVERT: M 771 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7529 (mmt90) REVERT: M 779 MET cc_start: 0.7502 (tmm) cc_final: 0.6965 (tmm) REVERT: M 781 ASP cc_start: 0.6985 (t0) cc_final: 0.6617 (t0) REVERT: M 880 MET cc_start: 0.7284 (ptp) cc_final: 0.7078 (mtm) REVERT: N 51 ASP cc_start: 0.6703 (m-30) cc_final: 0.5800 (p0) REVERT: N 323 VAL cc_start: 0.6331 (OUTLIER) cc_final: 0.5923 (p) REVERT: N 324 TRP cc_start: 0.7378 (m-90) cc_final: 0.6945 (m-90) REVERT: N 340 GLU cc_start: 0.7449 (tp30) cc_final: 0.7237 (tp30) REVERT: N 342 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6976 (mm-30) REVERT: N 371 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.3460 (tp) REVERT: K 641 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7567 (t70) REVERT: K 670 ILE cc_start: 0.8499 (mt) cc_final: 0.8243 (mp) REVERT: K 694 HIS cc_start: 0.7684 (m90) cc_final: 0.7436 (m-70) REVERT: K 829 LYS cc_start: 0.7325 (mmmm) cc_final: 0.7016 (mmmm) REVERT: K 855 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7431 (mmmt) REVERT: K 885 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6778 (ttt180) outliers start: 29 outliers final: 23 residues processed: 306 average time/residue: 0.2100 time to fit residues: 89.2131 Evaluate side-chains 316 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 541 CYS Chi-restraints excluded: chain M residue 669 SER Chi-restraints excluded: chain M residue 771 ARG Chi-restraints excluded: chain M residue 775 SER Chi-restraints excluded: chain M residue 776 ASN Chi-restraints excluded: chain M residue 862 THR Chi-restraints excluded: chain M residue 898 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 228 VAL Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 323 VAL Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain K residue 641 ASP Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 687 VAL Chi-restraints excluded: chain K residue 727 THR Chi-restraints excluded: chain K residue 758 VAL Chi-restraints excluded: chain K residue 862 THR Chi-restraints excluded: chain K residue 882 ARG Chi-restraints excluded: chain K residue 885 ARG Chi-restraints excluded: chain L residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 90 optimal weight: 100.0000 chunk 23 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 176 optimal weight: 0.4980 chunk 122 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 171 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.199683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155151 restraints weight = 40248.065| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.59 r_work: 0.3769 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24284 Z= 0.151 Angle : 0.585 10.155 34256 Z= 0.325 Chirality : 0.037 0.292 3787 Planarity : 0.004 0.060 3212 Dihedral : 27.889 179.726 5847 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 13.68 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.90 (0.19), residues: 1987 helix: 1.78 (0.17), residues: 968 sheet: 0.15 (0.47), residues: 119 loop : -0.65 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 99 TYR 0.020 0.001 TYR K 660 PHE 0.042 0.001 PHE N 261 TRP 0.016 0.001 TRP K 860 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00334 (24260) covalent geometry : angle 0.57555 (34220) hydrogen bonds : bond 0.03489 ( 1135) hydrogen bonds : angle 3.35660 ( 2872) metal coordination : bond 0.00571 ( 24) metal coordination : angle 3.24910 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6588.66 seconds wall clock time: 112 minutes 59.43 seconds (6779.43 seconds total)