Starting phenix.real_space_refine on Sat Sep 12 05:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.cif Found real_map, /net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.map" model { file = "/net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6upk_20840/09_2026/6upk_20840.cif" } resolution = 4.9 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= 0.005 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 44 5.16 5 C 8349 2.51 5 N 2497 2.21 5 O 2827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13861 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain breaks: 2 Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2241 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 1364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1358 Classifications: {'peptide': 167} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1358 Classifications: {'peptide': 167} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1379 Chain: "H" Number of atoms: 1962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 244, 1956 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 13, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 244, 1956 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 13, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 1994 Chain: "I" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1466 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1486 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER H 86 " occ=0.66 ... (10 atoms not shown) pdb=" OG BSER H 86 " occ=0.34 residue: pdb=" N ACYS H 207 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYS H 207 " occ=0.39 Time building chain proxies: 3.23, per 1000 atoms: 0.23 Number of scatterers: 13861 At special positions: 0 Unit cell: (95.4045, 120.659, 165.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 144 15.00 O 2827 8.00 N 2497 7.00 C 8349 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 Links applied TRANS " UNK G 634 " - " LYS G 633 " " UNK G 926 " - " LEU G 925 " " UNK H 172 " - " GLN H 171 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 611.2 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 16 sheets defined 39.6% alpha, 17.8% beta 65 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.921A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.872A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.650A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 77 removed outlier: 4.211A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.970A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.557A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.137A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.763A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.756A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.205A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 4.191A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 115 removed outlier: 3.925A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 4.655A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.940A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.244A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.685A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 636 removed outlier: 4.396A pdb=" N ILE G 624 " --> pdb=" O ASN G 620 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 625 " --> pdb=" O ALA G 621 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS G 626 " --> pdb=" O PHE G 622 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 628 " --> pdb=" O ILE G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 788 removed outlier: 3.635A pdb=" N GLN G 767 " --> pdb=" O LEU G 763 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 776 " --> pdb=" O MET G 772 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA G 779 " --> pdb=" O LYS G 775 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 890 Processing helix chain 'G' and resid 901 through 910 Processing helix chain 'G' and resid 916 through 924 removed outlier: 3.717A pdb=" N GLY G 920 " --> pdb=" O PHE G 917 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY G 921 " --> pdb=" O GLU G 918 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TRP G 922 " --> pdb=" O GLN G 919 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 removed outlier: 4.258A pdb=" N ASER H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 180 removed outlier: 3.549A pdb=" N UNK H 180 " --> pdb=" O UNK H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 Processing helix chain 'H' and resid 309 through 323 removed outlier: 3.796A pdb=" N SER H 315 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 317 " --> pdb=" O MET H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 407 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.269A 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 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 530 through 532 removed outlier: 3.722A pdb=" N TYR G 530 " --> pdb=" O ILE G 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 554 through 562 removed outlier: 6.642A pdb=" N GLU G 597 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL H 163 " --> pdb=" O GLU G 597 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR G 599 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 140 " --> pdb=" O THR H 147 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 138 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 698 through 700 removed outlier: 3.585A pdb=" N GLY G 686 " --> pdb=" O HIS G 683 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 665 " --> pdb=" O GLY G 678 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 680 " --> pdb=" O LYS G 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS G 663 " --> pdb=" O LEU G 680 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA G 682 " --> pdb=" O LYS G 661 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS G 661 " --> pdb=" O ALA G 682 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ASP G 664 " --> pdb=" O GLU G 743 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU G 743 " --> pdb=" O ASP G 664 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG G 734 " --> pdb=" O ASN G 726 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN G 726 " --> pdb=" O ARG G 734 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 736 " --> pdb=" O LEU G 724 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 738 " --> pdb=" O PHE G 722 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL G 719 " --> pdb=" O PHE G 709 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 709 " --> pdb=" O VAL G 719 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS G 721 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA G 707 " --> pdb=" O HIS G 721 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 723 " --> pdb=" O LYS G 705 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 806 through 808 removed outlier: 3.501A pdb=" N PHE G 833 " --> pdb=" O ASN G 826 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 870 through 874 removed outlier: 6.770A pdb=" N MET G 870 " --> pdb=" O ILE G 859 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 859 " --> pdb=" O MET G 870 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN G 872 " --> pdb=" O MET G 857 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET G 857 " --> pdb=" O ASN G 872 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N THR G 894 " --> pdb=" O GLU G 841 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE G 843 " --> pdb=" O THR G 894 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.597A pdb=" N ASP H 75 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 62 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS H 63 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE H 52 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114 removed outlier: 4.698A pdb=" N LEU H 119 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU H 130 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE H 121 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 239 through 246 removed outlier: 6.507A pdb=" N SER H 258 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU H 242 " --> pdb=" O VAL H 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL H 256 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU H 244 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE H 254 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN H 252 " --> pdb=" O PRO H 246 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS H 271 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ARG H 269 " --> pdb=" O PRO H 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'H' and resid 400 through 406 removed outlier: 6.520A pdb=" N PHE H 389 " --> pdb=" O SER H 405 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS H 426 " --> pdb=" O SER H 375 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL H 377 " --> pdb=" O LYS H 426 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3383 1.33 - 1.45: 3635 1.45 - 1.57: 7041 1.57 - 1.70: 286 1.70 - 1.82: 73 Bond restraints: 14418 Sorted by residual: bond pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT I 3 " pdb=" C2' DT I 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT I 12 " pdb=" C2' DT I 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG J -18 " pdb=" C2' DG J -18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 ... (remaining 14413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 19249 2.25 - 4.50: 736 4.50 - 6.75: 66 6.75 - 9.00: 10 9.00 - 11.26: 6 Bond angle restraints: 20067 Sorted by residual: angle pdb=" N TYR H 93 " pdb=" CA TYR H 93 " pdb=" C TYR H 93 " ideal model delta sigma weight residual 111.75 122.51 -10.76 1.28e+00 6.10e-01 7.07e+01 angle pdb=" N ILE G 586 " pdb=" CA ILE G 586 " pdb=" C ILE G 586 " ideal model delta sigma weight residual 111.91 105.33 6.58 8.90e-01 1.26e+00 5.46e+01 angle pdb=" N THR H 170 " pdb=" CA THR H 170 " pdb=" C THR H 170 " ideal model delta sigma weight residual 111.28 102.21 9.07 1.35e+00 5.49e-01 4.51e+01 angle pdb=" N TYR E 41 " pdb=" CA TYR E 41 " pdb=" C TYR E 41 " ideal model delta sigma weight residual 110.50 119.93 -9.43 1.41e+00 5.03e-01 4.47e+01 angle pdb=" C LYS H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.70 132.96 -11.26 1.80e+00 3.09e-01 3.91e+01 ... (remaining 20062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 7400 27.34 - 54.68: 770 54.68 - 82.01: 148 82.01 - 109.35: 3 109.35 - 136.69: 2 Dihedral angle restraints: 8323 sinusoidal: 4337 harmonic: 3986 Sorted by residual: dihedral pdb=" CA PHE H 165 " pdb=" C PHE H 165 " pdb=" N TYR H 166 " pdb=" CA TYR H 166 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA TYR H 11 " pdb=" C TYR H 11 " pdb=" N GLN H 12 " pdb=" CA GLN H 12 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE H 89 " pdb=" C PHE H 89 " pdb=" N LYS H 90 " pdb=" CA LYS H 90 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 8320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2072 0.097 - 0.193: 165 0.193 - 0.290: 8 0.290 - 0.386: 2 0.386 - 0.482: 2 Chirality restraints: 2249 Sorted by residual: chirality pdb=" CB VAL H 362 " pdb=" CA VAL H 362 " pdb=" CG1 VAL H 362 " pdb=" CG2 VAL H 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA TYR H 93 " pdb=" N TYR H 93 " pdb=" C TYR H 93 " pdb=" CB TYR H 93 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE G 718 " pdb=" CA ILE G 718 " pdb=" CG1 ILE G 718 " pdb=" CG2 ILE G 718 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2246 not shown) Planarity restraints: 2064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 167 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C VAL H 167 " 0.070 2.00e-02 2.50e+03 pdb=" O VAL H 167 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO H 168 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 92 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS H 92 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS H 92 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR H 93 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " -0.023 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR D 40 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.000 2.00e-02 2.50e+03 ... (remaining 2061 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 27 2.24 - 2.90: 5241 2.90 - 3.57: 21765 3.57 - 4.23: 36651 4.23 - 4.90: 54899 Nonbonded interactions: 118583 Sorted by model distance: nonbonded pdb=" NZ LYS G 626 " pdb=" OP1 DT I -6 " model vdw 1.570 3.120 nonbonded pdb=" NE2 GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.571 3.120 nonbonded pdb=" CG GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.687 3.440 nonbonded pdb=" NH1 ARG E 40 " pdb=" N2 DG J -8 " model vdw 1.734 3.200 nonbonded pdb=" CD GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.833 3.270 ... (remaining 118578 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 'B' selection = (chain 'F' and resid 25 through 102) } 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.006 0.076 14421 Z= 0.413 Angle : 0.994 11.256 20076 Z= 0.672 Chirality : 0.057 0.482 2249 Planarity : 0.007 0.064 2061 Dihedral : 20.423 136.691 5738 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -3.94 (0.19), residues: 1292 helix: -2.50 (0.17), residues: 446 sheet: -3.00 (0.34), residues: 169 loop : -2.58 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 79 TYR 0.046 0.004 TYR D 40 PHE 0.037 0.003 PHE H 222 TRP 0.024 0.003 TRP G 902 HIS 0.009 0.002 HIS H 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.41 (14418) covalent geometry : angle 0.99429 / 0.67 (20067) hydrogen bonds : bond 0.18724 / 12.09 ( 587) hydrogen bonds : angle 8.33307 / 5.67 ( 1475) link_TRANS : bond 0.00336 / 0.17 ( 3) link_TRANS : angle 0.74565 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.456 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9866 (mt-10) cc_final: 0.9598 (mp0) REVERT: A 99 TYR cc_start: 0.9380 (t80) cc_final: 0.8876 (t80) REVERT: A 129 ARG cc_start: 0.9575 (mtt180) cc_final: 0.9007 (ttm110) REVERT: B 50 ILE cc_start: 0.9300 (mm) cc_final: 0.8839 (mm) REVERT: B 61 PHE cc_start: 0.9595 (t80) cc_final: 0.9337 (t80) REVERT: B 68 ASP cc_start: 0.9072 (p0) cc_final: 0.8815 (p0) REVERT: D 37 TYR cc_start: 0.9109 (m-80) cc_final: 0.8849 (m-80) REVERT: D 82 HIS cc_start: 0.9774 (t-90) cc_final: 0.9522 (m90) REVERT: E 67 PHE cc_start: 0.9506 (t80) cc_final: 0.9134 (t80) REVERT: E 94 GLU cc_start: 0.9712 (tp30) cc_final: 0.9452 (tt0) REVERT: F 84 MET cc_start: 0.9609 (mmp) cc_final: 0.9406 (mpp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1360 time to fit residues: 25.8930 Evaluate side-chains 91 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN B 64 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 110 ASN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 93 GLN F 25 ASN G 585 ASN H 12 GLN H 60 HIS H 144 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038690 restraints weight = 439047.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.040469 restraints weight = 153611.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041540 restraints weight = 77956.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042214 restraints weight = 48522.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.042551 restraints weight = 34606.298| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14421 Z= 0.188 Angle : 0.725 11.588 20076 Z= 0.407 Chirality : 0.046 0.258 2249 Planarity : 0.006 0.060 2061 Dihedral : 25.891 136.259 3072 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -2.95 (0.21), residues: 1292 helix: -1.18 (0.21), residues: 468 sheet: -2.61 (0.35), residues: 175 loop : -2.34 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 55 TYR 0.019 0.002 TYR D 40 PHE 0.013 0.002 PHE H 415 TRP 0.018 0.002 TRP G 902 HIS 0.007 0.001 HIS H 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 (14418) covalent geometry : angle 0.72548 / 0.41 (20067) hydrogen bonds : bond 0.10346 / 7.14 ( 587) hydrogen bonds : angle 6.79143 / 4.56 ( 1475) link_TRANS : bond 0.00213 / 0.11 ( 3) link_TRANS : angle 0.64311 / 0.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.382 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8892 (t80) cc_final: 0.8443 (t80) REVERT: A 105 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9273 (pt0) REVERT: B 61 PHE cc_start: 0.9219 (t80) cc_final: 0.8800 (t80) REVERT: B 68 ASP cc_start: 0.8654 (p0) cc_final: 0.8161 (p0) REVERT: D 106 LEU cc_start: 0.9728 (tt) cc_final: 0.9477 (tt) REVERT: E 62 ILE cc_start: 0.9029 (mm) cc_final: 0.8769 (mm) REVERT: E 67 PHE cc_start: 0.9216 (t80) cc_final: 0.8469 (t80) REVERT: E 93 GLN cc_start: 0.9544 (tt0) cc_final: 0.9131 (tt0) REVERT: E 94 GLU cc_start: 0.9674 (tp30) cc_final: 0.9279 (tt0) REVERT: E 122 LYS cc_start: 0.9711 (mtpp) cc_final: 0.9446 (mtmm) REVERT: G 906 MET cc_start: 0.8064 (mmt) cc_final: 0.7617 (mmp) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1348 time to fit residues: 23.0835 Evaluate side-chains 87 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 22 optimal weight: 7.9990 chunk 144 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 133 optimal weight: 30.0000 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.037429 restraints weight = 472813.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039250 restraints weight = 159183.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.040309 restraints weight = 79426.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040977 restraints weight = 48720.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.041396 restraints weight = 34528.442| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14421 Z= 0.174 Angle : 0.679 10.144 20076 Z= 0.381 Chirality : 0.044 0.248 2249 Planarity : 0.005 0.067 2061 Dihedral : 26.112 137.779 3072 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -2.49 (0.22), residues: 1292 helix: -0.63 (0.22), residues: 477 sheet: -2.53 (0.36), residues: 169 loop : -2.20 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 569 TYR 0.017 0.002 TYR H 166 PHE 0.016 0.002 PHE H 150 TRP 0.018 0.002 TRP G 902 HIS 0.006 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (14418) covalent geometry : angle 0.67932 / 0.38 (20067) hydrogen bonds : bond 0.09307 / 6.42 ( 587) hydrogen bonds : angle 6.43968 / 4.32 ( 1475) link_TRANS : bond 0.00181 / 0.09 ( 3) link_TRANS : angle 0.60273 / 0.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.475 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: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8772 (p0) cc_final: 0.8051 (p0) REVERT: C 50 TYR cc_start: 0.9151 (t80) cc_final: 0.8843 (t80) REVERT: C 95 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9228 (pptt) REVERT: E 62 ILE cc_start: 0.9017 (mm) cc_final: 0.8780 (mm) REVERT: E 67 PHE cc_start: 0.9245 (t80) cc_final: 0.8291 (t80) REVERT: E 93 GLN cc_start: 0.9552 (tt0) cc_final: 0.9042 (tt0) REVERT: E 94 GLU cc_start: 0.9713 (tp30) cc_final: 0.9331 (tt0) REVERT: G 906 MET cc_start: 0.8052 (mmt) cc_final: 0.7654 (mmp) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.1260 time to fit residues: 20.6547 Evaluate side-chains 77 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 64 optimal weight: 40.0000 chunk 80 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 56 optimal weight: 0.0050 chunk 33 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.038566 restraints weight = 455907.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040436 restraints weight = 153195.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041492 restraints weight = 75885.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042202 restraints weight = 46281.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.042545 restraints weight = 32639.625| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14421 Z= 0.129 Angle : 0.633 9.983 20076 Z= 0.354 Chirality : 0.045 0.256 2249 Planarity : 0.005 0.061 2061 Dihedral : 26.115 137.637 3072 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -2.12 (0.22), residues: 1292 helix: -0.20 (0.23), residues: 480 sheet: -2.42 (0.35), residues: 178 loop : -2.06 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 569 TYR 0.019 0.002 TYR H 219 PHE 0.016 0.001 PHE H 222 TRP 0.014 0.002 TRP G 922 HIS 0.006 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (14418) covalent geometry : angle 0.63274 / 0.35 (20067) hydrogen bonds : bond 0.08870 / 6.10 ( 587) hydrogen bonds : angle 6.01492 / 4.04 ( 1475) link_TRANS : bond 0.00154 / 0.08 ( 3) link_TRANS : angle 0.64045 / 0.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.486 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9616 (t80) cc_final: 0.9296 (t80) REVERT: B 68 ASP cc_start: 0.8592 (p0) cc_final: 0.7842 (p0) REVERT: C 50 TYR cc_start: 0.9164 (t80) cc_final: 0.8925 (t80) REVERT: C 95 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9235 (pptt) REVERT: D 106 LEU cc_start: 0.9722 (tt) cc_final: 0.9463 (tt) REVERT: E 62 ILE cc_start: 0.9321 (mm) cc_final: 0.9066 (mm) REVERT: E 67 PHE cc_start: 0.9200 (t80) cc_final: 0.8554 (t80) REVERT: E 89 VAL cc_start: 0.9796 (t) cc_final: 0.9449 (p) REVERT: E 90 MET cc_start: 0.9621 (mmp) cc_final: 0.9392 (mmm) REVERT: E 93 GLN cc_start: 0.9574 (tt0) cc_final: 0.9203 (tt0) REVERT: E 94 GLU cc_start: 0.9680 (tp30) cc_final: 0.9151 (tt0) REVERT: G 906 MET cc_start: 0.7950 (mmt) cc_final: 0.7518 (mmp) REVERT: H 253 MET cc_start: 0.9061 (mmp) cc_final: 0.8690 (mmm) REVERT: H 289 MET cc_start: 0.9088 (mpp) cc_final: 0.8726 (mpp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1189 time to fit residues: 21.3831 Evaluate side-chains 82 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 87 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038521 restraints weight = 398303.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039972 restraints weight = 172128.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.040443 restraints weight = 74622.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040569 restraints weight = 57344.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040837 restraints weight = 52238.655| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14421 Z= 0.151 Angle : 0.629 9.207 20076 Z= 0.354 Chirality : 0.043 0.249 2249 Planarity : 0.005 0.062 2061 Dihedral : 26.103 137.269 3072 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.91 (0.22), residues: 1292 helix: 0.08 (0.23), residues: 478 sheet: -2.32 (0.37), residues: 168 loop : -2.04 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 131 TYR 0.016 0.002 TYR D 121 PHE 0.012 0.001 PHE H 415 TRP 0.015 0.002 TRP G 922 HIS 0.008 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (14418) covalent geometry : angle 0.62863 / 0.35 (20067) hydrogen bonds : bond 0.08603 / 5.94 ( 587) hydrogen bonds : angle 5.89905 / 3.95 ( 1475) link_TRANS : bond 0.00179 / 0.09 ( 3) link_TRANS : angle 0.63406 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.495 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8742 (p0) cc_final: 0.7966 (p0) REVERT: C 50 TYR cc_start: 0.9192 (t80) cc_final: 0.8897 (t80) REVERT: C 95 LYS cc_start: 0.9486 (ttmm) cc_final: 0.9233 (pptt) REVERT: E 50 GLU cc_start: 0.9570 (pt0) cc_final: 0.9358 (tp30) REVERT: E 62 ILE cc_start: 0.9283 (mm) cc_final: 0.8953 (mm) REVERT: E 67 PHE cc_start: 0.9265 (t80) cc_final: 0.8445 (t80) REVERT: E 93 GLN cc_start: 0.9627 (tt0) cc_final: 0.9010 (tt0) REVERT: E 94 GLU cc_start: 0.9713 (tp30) cc_final: 0.9229 (tt0) REVERT: G 559 MET cc_start: 0.8888 (tmm) cc_final: 0.8228 (tmm) REVERT: G 906 MET cc_start: 0.7753 (mmt) cc_final: 0.7167 (mmp) REVERT: H 253 MET cc_start: 0.9108 (mmp) cc_final: 0.8164 (mpp) REVERT: H 289 MET cc_start: 0.9102 (mpp) cc_final: 0.8803 (mpp) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.1188 time to fit residues: 19.0320 Evaluate side-chains 76 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 93 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 71 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038214 restraints weight = 433581.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040032 restraints weight = 178893.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040870 restraints weight = 70160.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040786 restraints weight = 54507.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040898 restraints weight = 50058.526| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14421 Z= 0.130 Angle : 0.605 8.129 20076 Z= 0.341 Chirality : 0.043 0.244 2249 Planarity : 0.004 0.059 2061 Dihedral : 26.142 137.998 3072 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.74 (0.23), residues: 1292 helix: 0.24 (0.23), residues: 480 sheet: -2.32 (0.36), residues: 179 loop : -1.90 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 569 TYR 0.019 0.002 TYR H 219 PHE 0.028 0.001 PHE H 222 TRP 0.015 0.002 TRP G 922 HIS 0.004 0.001 HIS H 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (14418) covalent geometry : angle 0.60458 / 0.34 (20067) hydrogen bonds : bond 0.08348 / 5.75 ( 587) hydrogen bonds : angle 5.67930 / 3.83 ( 1475) link_TRANS : bond 0.00157 / 0.08 ( 3) link_TRANS : angle 0.63399 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.480 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 CYS cc_start: 0.9741 (t) cc_final: 0.9389 (t) REVERT: A 97 GLU cc_start: 0.9748 (mt-10) cc_final: 0.9442 (mm-30) REVERT: A 110 CYS cc_start: 0.9367 (m) cc_final: 0.9161 (m) REVERT: B 68 ASP cc_start: 0.8741 (p0) cc_final: 0.7971 (p0) REVERT: C 50 TYR cc_start: 0.9225 (t80) cc_final: 0.8893 (t80) REVERT: C 95 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9234 (pptt) REVERT: E 62 ILE cc_start: 0.9250 (mm) cc_final: 0.9006 (mm) REVERT: E 67 PHE cc_start: 0.9224 (t80) cc_final: 0.8365 (t80) REVERT: E 93 GLN cc_start: 0.9657 (tt0) cc_final: 0.9114 (tt0) REVERT: E 94 GLU cc_start: 0.9717 (tp30) cc_final: 0.9225 (tt0) REVERT: F 84 MET cc_start: 0.9613 (mpp) cc_final: 0.9395 (mpp) REVERT: G 870 MET cc_start: 0.6992 (tpp) cc_final: 0.6649 (tpp) REVERT: G 906 MET cc_start: 0.7696 (mmt) cc_final: 0.7037 (mmp) REVERT: H 253 MET cc_start: 0.9063 (mmp) cc_final: 0.8180 (mpp) REVERT: H 289 MET cc_start: 0.9075 (mpp) cc_final: 0.8803 (mpp) REVERT: H 313 MET cc_start: 0.9141 (ttm) cc_final: 0.8595 (mtp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1151 time to fit residues: 18.8092 Evaluate side-chains 81 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 604 ASN G 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.021977 restraints weight = 297158.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.023170 restraints weight = 155125.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.023993 restraints weight = 98829.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.024555 restraints weight = 70907.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.024937 restraints weight = 55356.793| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14421 Z= 0.225 Angle : 0.711 11.429 20076 Z= 0.397 Chirality : 0.045 0.256 2249 Planarity : 0.005 0.061 2061 Dihedral : 26.293 138.558 3072 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.90 (0.22), residues: 1292 helix: 0.07 (0.23), residues: 481 sheet: -2.56 (0.35), residues: 179 loop : -1.91 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 211 TYR 0.033 0.002 TYR E 54 PHE 0.013 0.002 PHE H 403 TRP 0.017 0.002 TRP G 922 HIS 0.007 0.002 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (14418) covalent geometry : angle 0.71060 / 0.40 (20067) hydrogen bonds : bond 0.09332 / 6.37 ( 587) hydrogen bonds : angle 5.97364 / 4.03 ( 1475) link_TRANS : bond 0.00235 / 0.12 ( 3) link_TRANS : angle 0.63059 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.489 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: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9741 (t80) cc_final: 0.9443 (t80) REVERT: A 96 CYS cc_start: 0.9861 (t) cc_final: 0.9600 (t) REVERT: A 97 GLU cc_start: 0.9813 (mt-10) cc_final: 0.9527 (mm-30) REVERT: C 50 TYR cc_start: 0.9487 (t80) cc_final: 0.8962 (t80) REVERT: E 67 PHE cc_start: 0.9313 (t80) cc_final: 0.8761 (t80) REVERT: E 93 GLN cc_start: 0.9703 (tt0) cc_final: 0.9385 (tt0) REVERT: E 94 GLU cc_start: 0.9772 (tp30) cc_final: 0.9391 (tt0) REVERT: G 559 MET cc_start: 0.8749 (tmm) cc_final: 0.8388 (tmm) REVERT: H 289 MET cc_start: 0.8972 (mpp) cc_final: 0.8724 (mpp) REVERT: H 313 MET cc_start: 0.9102 (ttm) cc_final: 0.8693 (mtp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1155 time to fit residues: 17.7968 Evaluate side-chains 76 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037434 restraints weight = 405984.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039157 restraints weight = 141035.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.040146 restraints weight = 71222.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040778 restraints weight = 43695.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.041147 restraints weight = 31302.477| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14421 Z= 0.124 Angle : 0.631 8.487 20076 Z= 0.352 Chirality : 0.044 0.242 2249 Planarity : 0.005 0.064 2061 Dihedral : 26.317 139.320 3072 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.60 (0.23), residues: 1292 helix: 0.25 (0.23), residues: 485 sheet: -2.26 (0.37), residues: 172 loop : -1.75 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 569 TYR 0.042 0.002 TYR B 72 PHE 0.015 0.002 PHE H 415 TRP 0.015 0.002 TRP G 922 HIS 0.004 0.001 HIS H 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (14418) covalent geometry : angle 0.63074 / 0.35 (20067) hydrogen bonds : bond 0.08420 / 5.72 ( 587) hydrogen bonds : angle 5.55592 / 3.74 ( 1475) link_TRANS : bond 0.00154 / 0.08 ( 3) link_TRANS : angle 0.60996 / 0.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.496 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9641 (t80) cc_final: 0.9394 (t80) REVERT: A 96 CYS cc_start: 0.9757 (t) cc_final: 0.9366 (t) REVERT: A 97 GLU cc_start: 0.9693 (mt-10) cc_final: 0.9398 (mm-30) REVERT: A 110 CYS cc_start: 0.9357 (m) cc_final: 0.8587 (t) REVERT: B 68 ASP cc_start: 0.8803 (p0) cc_final: 0.8598 (p0) REVERT: D 59 MET cc_start: 0.9402 (ttm) cc_final: 0.9169 (mtp) REVERT: E 67 PHE cc_start: 0.9145 (t80) cc_final: 0.8265 (t80) REVERT: E 89 VAL cc_start: 0.9803 (t) cc_final: 0.9461 (p) REVERT: E 90 MET cc_start: 0.9552 (mmp) cc_final: 0.9315 (mmm) REVERT: E 93 GLN cc_start: 0.9647 (tt0) cc_final: 0.9034 (tp40) REVERT: E 94 GLU cc_start: 0.9715 (tp30) cc_final: 0.9204 (tt0) REVERT: F 84 MET cc_start: 0.9632 (mpp) cc_final: 0.9382 (mpp) REVERT: G 559 MET cc_start: 0.8984 (tmm) cc_final: 0.8500 (tmm) REVERT: H 253 MET cc_start: 0.9062 (mmp) cc_final: 0.8045 (mpp) REVERT: H 289 MET cc_start: 0.8913 (mpp) cc_final: 0.8649 (mpp) REVERT: H 313 MET cc_start: 0.9105 (ttm) cc_final: 0.8610 (mtp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1246 time to fit residues: 21.3339 Evaluate side-chains 80 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 121 optimal weight: 0.0670 chunk 71 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.036303 restraints weight = 409735.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038026 restraints weight = 148769.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.038703 restraints weight = 63057.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038885 restraints weight = 41648.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038934 restraints weight = 41926.896| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14421 Z= 0.159 Angle : 0.649 8.850 20076 Z= 0.363 Chirality : 0.043 0.236 2249 Planarity : 0.004 0.053 2061 Dihedral : 26.294 137.832 3072 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.57 (0.23), residues: 1292 helix: 0.31 (0.24), residues: 484 sheet: -2.31 (0.36), residues: 179 loop : -1.73 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 569 TYR 0.021 0.002 TYR E 54 PHE 0.012 0.001 PHE H 89 TRP 0.020 0.002 TRP G 922 HIS 0.007 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (14418) covalent geometry : angle 0.64946 / 0.36 (20067) hydrogen bonds : bond 0.08277 / 5.68 ( 587) hydrogen bonds : angle 5.69896 / 3.85 ( 1475) link_TRANS : bond 0.00179 / 0.09 ( 3) link_TRANS : angle 0.61634 / 0.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.504 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: symmetry clash REVERT: A 67 PHE cc_start: 0.9739 (t80) cc_final: 0.9443 (t80) REVERT: A 96 CYS cc_start: 0.9847 (t) cc_final: 0.9552 (t) REVERT: A 97 GLU cc_start: 0.9762 (mt-10) cc_final: 0.9486 (mm-30) REVERT: A 110 CYS cc_start: 0.9317 (m) cc_final: 0.8607 (t) REVERT: B 68 ASP cc_start: 0.8993 (p0) cc_final: 0.8603 (p0) REVERT: E 67 PHE cc_start: 0.9222 (t80) cc_final: 0.8658 (t80) REVERT: E 89 VAL cc_start: 0.9819 (t) cc_final: 0.9609 (t) REVERT: E 93 GLN cc_start: 0.9691 (tt0) cc_final: 0.9371 (tt0) REVERT: E 94 GLU cc_start: 0.9772 (tp30) cc_final: 0.9355 (tt0) REVERT: H 253 MET cc_start: 0.9009 (mmp) cc_final: 0.8668 (mmp) REVERT: H 313 MET cc_start: 0.9072 (ttm) cc_final: 0.8677 (mtp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1176 time to fit residues: 18.1091 Evaluate side-chains 73 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.035909 restraints weight = 455250.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037665 restraints weight = 146928.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038127 restraints weight = 70567.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038488 restraints weight = 42870.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038594 restraints weight = 40341.905| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14421 Z= 0.154 Angle : 0.643 8.567 20076 Z= 0.360 Chirality : 0.043 0.247 2249 Planarity : 0.005 0.060 2061 Dihedral : 26.404 139.016 3072 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.59 (0.23), residues: 1292 helix: 0.27 (0.24), residues: 485 sheet: -2.15 (0.37), residues: 170 loop : -1.78 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 569 TYR 0.019 0.002 TYR E 54 PHE 0.011 0.001 PHE H 415 TRP 0.017 0.002 TRP G 922 HIS 0.007 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (14418) covalent geometry : angle 0.64281 / 0.36 (20067) hydrogen bonds : bond 0.08143 / 5.57 ( 587) hydrogen bonds : angle 5.65051 / 3.84 ( 1475) link_TRANS : bond 0.00169 / 0.09 ( 3) link_TRANS : angle 0.59819 / 0.30 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.487 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: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9677 (t80) cc_final: 0.9441 (t80) REVERT: A 96 CYS cc_start: 0.9777 (t) cc_final: 0.9452 (t) REVERT: A 97 GLU cc_start: 0.9690 (mt-10) cc_final: 0.9446 (mm-30) REVERT: A 110 CYS cc_start: 0.9317 (m) cc_final: 0.8613 (t) REVERT: A 120 MET cc_start: 0.9337 (tmm) cc_final: 0.9070 (tmm) REVERT: A 122 LYS cc_start: 0.9585 (ttpt) cc_final: 0.9058 (tttt) REVERT: E 67 PHE cc_start: 0.9130 (t80) cc_final: 0.8558 (t80) REVERT: E 89 VAL cc_start: 0.9803 (t) cc_final: 0.9595 (t) REVERT: E 93 GLN cc_start: 0.9725 (tt0) cc_final: 0.9364 (tt0) REVERT: E 94 GLU cc_start: 0.9747 (tp30) cc_final: 0.9275 (tt0) REVERT: G 559 MET cc_start: 0.8874 (tmm) cc_final: 0.8412 (tmm) REVERT: H 253 MET cc_start: 0.9011 (mmp) cc_final: 0.8667 (mmp) REVERT: H 289 MET cc_start: 0.8927 (mpp) cc_final: 0.8457 (mpp) REVERT: H 313 MET cc_start: 0.9095 (ttm) cc_final: 0.8645 (mtp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1192 time to fit residues: 18.8411 Evaluate side-chains 77 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 135 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.038210 restraints weight = 333823.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039897 restraints weight = 130794.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040545 restraints weight = 57936.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.040679 restraints weight = 37207.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040854 restraints weight = 36998.659| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14421 Z= 0.119 Angle : 0.618 7.589 20076 Z= 0.345 Chirality : 0.044 0.236 2249 Planarity : 0.004 0.056 2061 Dihedral : 26.365 138.347 3072 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -1.44 (0.23), residues: 1292 helix: 0.38 (0.24), residues: 485 sheet: -1.99 (0.38), residues: 170 loop : -1.71 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 569 TYR 0.019 0.001 TYR B 88 PHE 0.013 0.001 PHE H 415 TRP 0.018 0.002 TRP G 922 HIS 0.005 0.001 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (14418) covalent geometry : angle 0.61756 / 0.34 (20067) hydrogen bonds : bond 0.08277 / 5.66 ( 587) hydrogen bonds : angle 5.35693 / 3.64 ( 1475) link_TRANS : bond 0.00156 / 0.08 ( 3) link_TRANS : angle 0.59312 / 0.30 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.94 seconds wall clock time: 40 minutes 57.50 seconds (2457.50 seconds total)