Starting phenix.real_space_refine on Thu Jul 31 21:55:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6upk_20840/07_2025/6upk_20840.cif Found real_map, /net/cci-nas-00/data/ceres_data/6upk_20840/07_2025/6upk_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_20840/07_2025/6upk_20840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6upk_20840/07_2025/6upk_20840.map" model { file = "/net/cci-nas-00/data/ceres_data/6upk_20840/07_2025/6upk_20840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6upk_20840/07_2025/6upk_20840.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} 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: 21.51, per 1000 atoms: 1.55 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: 5.97 Conformation dependent library (CDL) restraints added in 5.0 seconds 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: 10.74 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: 10.14 Time building geometry restraints manager: 7.10 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=" CA GLU H 299 " pdb=" C GLU H 299 " ideal model delta sigma weight residual 1.523 1.558 -0.034 1.34e-02 5.57e+03 6.56e+00 bond pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.58e+00 bond pdb=" C TYR H 93 " pdb=" N ARG H 94 " ideal model delta sigma weight residual 1.333 1.306 0.028 1.43e-02 4.89e+03 3.74e+00 bond pdb=" C LYS H 100 " pdb=" N ASP H 101 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.40e-02 5.10e+03 3.29e+00 bond pdb=" N GLU H 299 " pdb=" CA GLU H 299 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.13e+00 ... (remaining 14413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 19345 2.25 - 4.50: 640 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: 2085 0.097 - 0.193: 152 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: 109.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 70.670 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.005 0.076 14421 Z= 0.266 Angle : 0.939 11.256 20076 Z= 0.553 Chirality : 0.053 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP G 902 HIS 0.009 0.002 HIS H 247 PHE 0.037 0.003 PHE H 222 TYR 0.046 0.004 TYR D 40 ARG 0.013 0.001 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00336 ( 3) link_TRANS : angle 0.74565 ( 9) hydrogen bonds : bond 0.18724 ( 587) hydrogen bonds : angle 8.33307 ( 1475) covalent geometry : bond 0.00541 (14418) covalent geometry : angle 0.93929 (20067) *********************** 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 : 2.871 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: 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: 0.8840 (mm) REVERT: B 61 PHE cc_start: 0.9595 (t80) cc_final: 0.9338 (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: 0.9521 (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: 0.4307 time to fit residues: 82.5637 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 : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN G 585 ASN G 604 ASN G 619 GLN H 12 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.033803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.021900 restraints weight = 427970.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.023274 restraints weight = 193918.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.024249 restraints weight = 115842.607| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14421 Z= 0.247 Angle : 0.723 11.466 20076 Z= 0.405 Chirality : 0.043 0.242 2249 Planarity : 0.006 0.060 2061 Dihedral : 26.238 140.677 3072 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.09 % Allowed : 1.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.21), residues: 1292 helix: -0.93 (0.21), residues: 476 sheet: -2.86 (0.36), residues: 157 loop : -2.32 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 902 HIS 0.007 0.002 HIS F 75 PHE 0.017 0.002 PHE H 403 TYR 0.021 0.003 TYR D 121 ARG 0.009 0.001 ARG F 67 Details of bonding type rmsd link_TRANS : bond 0.00202 ( 3) link_TRANS : angle 0.76437 ( 9) hydrogen bonds : bond 0.09211 ( 587) hydrogen bonds : angle 6.47638 ( 1475) covalent geometry : bond 0.00515 (14418) covalent geometry : angle 0.72292 (20067) *********************** 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 116 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.264 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: 0.9320 (t80) cc_final: 0.8835 (t80) REVERT: A 110 CYS cc_start: 0.9244 (m) cc_final: 0.8820 (m) REVERT: B 63 GLU cc_start: 0.9325 (pt0) cc_final: 0.9053 (pt0) REVERT: B 68 ASP cc_start: 0.8806 (p0) cc_final: 0.8281 (p0) REVERT: C 50 TYR cc_start: 0.9292 (t80) cc_final: 0.9089 (t80) REVERT: D 82 HIS cc_start: 0.9797 (t-90) cc_final: 0.9586 (m90) REVERT: E 62 ILE cc_start: 0.9275 (mm) cc_final: 0.8980 (mm) REVERT: E 67 PHE cc_start: 0.9352 (t80) cc_final: 0.8439 (t80) REVERT: E 93 GLN cc_start: 0.9687 (tt0) cc_final: 0.9168 (tp40) REVERT: E 94 GLU cc_start: 0.9798 (tp30) cc_final: 0.9537 (tt0) REVERT: E 122 LYS cc_start: 0.9859 (mtpp) cc_final: 0.9659 (mtmm) REVERT: H 253 MET cc_start: 0.9127 (mmp) cc_final: 0.8911 (mmm) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.2851 time to fit residues: 47.4685 Evaluate side-chains 85 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 136 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036658 restraints weight = 427026.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038182 restraints weight = 152855.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039311 restraints weight = 68949.728| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14421 Z= 0.153 Angle : 0.605 9.244 20076 Z= 0.342 Chirality : 0.040 0.237 2249 Planarity : 0.005 0.062 2061 Dihedral : 26.153 138.442 3072 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.09 % Allowed : 2.00 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.22), residues: 1292 helix: -0.04 (0.23), residues: 486 sheet: -2.49 (0.36), residues: 172 loop : -2.06 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 922 HIS 0.004 0.001 HIS H 247 PHE 0.013 0.001 PHE H 415 TYR 0.026 0.002 TYR B 72 ARG 0.010 0.001 ARG A 128 Details of bonding type rmsd link_TRANS : bond 0.00162 ( 3) link_TRANS : angle 0.64578 ( 9) hydrogen bonds : bond 0.07849 ( 587) hydrogen bonds : angle 5.82858 ( 1475) covalent geometry : bond 0.00319 (14418) covalent geometry : angle 0.60514 (20067) *********************** 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 124 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 2.603 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: A 67 PHE cc_start: 0.9636 (t80) cc_final: 0.9335 (t80) REVERT: A 99 TYR cc_start: 0.9154 (t80) cc_final: 0.8692 (t80) REVERT: B 63 GLU cc_start: 0.9163 (pt0) cc_final: 0.8688 (pt0) REVERT: B 68 ASP cc_start: 0.8808 (p0) cc_final: 0.8517 (p0) REVERT: B 72 TYR cc_start: 0.8857 (m-80) cc_final: 0.8571 (m-10) REVERT: C 50 TYR cc_start: 0.9186 (t80) cc_final: 0.8829 (t80) REVERT: D 106 LEU cc_start: 0.9755 (tt) cc_final: 0.9541 (tt) REVERT: E 67 PHE cc_start: 0.9205 (t80) cc_final: 0.8524 (t80) REVERT: E 93 GLN cc_start: 0.9655 (tt0) cc_final: 0.9307 (tt0) REVERT: E 94 GLU cc_start: 0.9722 (tp30) cc_final: 0.9215 (tt0) REVERT: G 870 MET cc_start: 0.7302 (tpt) cc_final: 0.6943 (tpp) REVERT: G 906 MET cc_start: 0.7521 (mmm) cc_final: 0.7253 (mmt) REVERT: H 289 MET cc_start: 0.9053 (mpp) cc_final: 0.8781 (mpp) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.3468 time to fit residues: 62.7396 Evaluate side-chains 82 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034675 restraints weight = 324903.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036120 restraints weight = 126593.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036985 restraints weight = 67038.152| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2502 r_free = 0.2502 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2502 r_free = 0.2502 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14421 Z= 0.188 Angle : 0.626 8.984 20076 Z= 0.353 Chirality : 0.041 0.212 2249 Planarity : 0.005 0.072 2061 Dihedral : 26.345 140.049 3072 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.22), residues: 1292 helix: 0.19 (0.23), residues: 485 sheet: -2.37 (0.37), residues: 165 loop : -1.97 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 922 HIS 0.011 0.001 HIS A 113 PHE 0.013 0.002 PHE H 403 TYR 0.018 0.002 TYR B 72 ARG 0.016 0.001 ARG E 129 Details of bonding type rmsd link_TRANS : bond 0.00170 ( 3) link_TRANS : angle 0.59312 ( 9) hydrogen bonds : bond 0.07988 ( 587) hydrogen bonds : angle 5.69676 ( 1475) covalent geometry : bond 0.00392 (14418) covalent geometry : angle 0.62573 (20067) *********************** 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 109 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.662 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: 0.9633 (t80) cc_final: 0.9341 (t80) REVERT: A 96 CYS cc_start: 0.9804 (t) cc_final: 0.9488 (t) REVERT: A 97 GLU cc_start: 0.9751 (mt-10) cc_final: 0.9509 (mm-30) REVERT: A 110 CYS cc_start: 0.9551 (m) cc_final: 0.9272 (m) REVERT: B 68 ASP cc_start: 0.8900 (p0) cc_final: 0.8616 (p0) REVERT: B 72 TYR cc_start: 0.8698 (m-80) cc_final: 0.8488 (m-10) REVERT: C 50 TYR cc_start: 0.9431 (t80) cc_final: 0.8910 (t80) REVERT: D 106 LEU cc_start: 0.9799 (tt) cc_final: 0.9590 (tt) REVERT: E 93 GLN cc_start: 0.9657 (tt0) cc_final: 0.9108 (tt0) REVERT: E 94 GLU cc_start: 0.9744 (tp30) cc_final: 0.9301 (tt0) REVERT: G 870 MET cc_start: 0.7725 (tpt) cc_final: 0.7521 (tpp) REVERT: H 289 MET cc_start: 0.8933 (mpp) cc_final: 0.8712 (mpp) REVERT: H 313 MET cc_start: 0.9143 (ttm) cc_final: 0.8624 (mtp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3228 time to fit residues: 51.8897 Evaluate side-chains 75 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 123 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 chunk 29 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 73 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 82 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.018959 restraints weight = 484935.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.020315 restraints weight = 214773.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.021213 restraints weight = 126624.658| |-----------------------------------------------------------------------------| r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2328 r_free = 0.2328 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2328 r_free = 0.2328 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14421 Z= 0.280 Angle : 0.737 11.361 20076 Z= 0.411 Chirality : 0.043 0.201 2249 Planarity : 0.006 0.060 2061 Dihedral : 26.979 142.451 3072 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 31.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1292 helix: -0.14 (0.22), residues: 484 sheet: -2.71 (0.34), residues: 179 loop : -2.04 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 902 HIS 0.011 0.002 HIS H 224 PHE 0.018 0.002 PHE H 403 TYR 0.024 0.002 TYR H 401 ARG 0.006 0.001 ARG B 67 Details of bonding type rmsd link_TRANS : bond 0.00235 ( 3) link_TRANS : angle 0.57565 ( 9) hydrogen bonds : bond 0.09217 ( 587) hydrogen bonds : angle 6.17217 ( 1475) covalent geometry : bond 0.00579 (14418) covalent geometry : angle 0.73674 (20067) *********************** 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 95 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.564 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: 0.9598 (t80) cc_final: 0.9199 (t80) REVERT: A 96 CYS cc_start: 0.9834 (t) cc_final: 0.9466 (t) REVERT: A 97 GLU cc_start: 0.9834 (mt-10) cc_final: 0.9452 (mm-30) REVERT: B 68 ASP cc_start: 0.8960 (p0) cc_final: 0.8715 (p0) REVERT: B 72 TYR cc_start: 0.8525 (m-80) cc_final: 0.8313 (m-10) REVERT: D 102 LEU cc_start: 0.9551 (tp) cc_final: 0.9349 (tp) REVERT: E 50 GLU cc_start: 0.9633 (pt0) cc_final: 0.9400 (pp20) REVERT: E 93 GLN cc_start: 0.9758 (tt0) cc_final: 0.9294 (tt0) REVERT: E 94 GLU cc_start: 0.9804 (tp30) cc_final: 0.9565 (tt0) REVERT: H 253 MET cc_start: 0.9095 (mmp) cc_final: 0.8410 (mtt) REVERT: H 313 MET cc_start: 0.9289 (ttm) cc_final: 0.8823 (mtp) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.3144 time to fit residues: 44.6461 Evaluate side-chains 67 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 122 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.032019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.020049 restraints weight = 436536.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.021455 restraints weight = 176625.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022448 restraints weight = 101805.220| |-----------------------------------------------------------------------------| r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14421 Z= 0.205 Angle : 0.642 8.584 20076 Z= 0.363 Chirality : 0.041 0.201 2249 Planarity : 0.005 0.065 2061 Dihedral : 27.015 140.051 3072 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.09 % Allowed : 1.39 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.22), residues: 1292 helix: 0.27 (0.23), residues: 483 sheet: -2.52 (0.35), residues: 175 loop : -1.92 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 922 HIS 0.008 0.001 HIS H 224 PHE 0.013 0.002 PHE H 403 TYR 0.037 0.002 TYR B 88 ARG 0.005 0.001 ARG G 569 Details of bonding type rmsd link_TRANS : bond 0.00174 ( 3) link_TRANS : angle 0.57736 ( 9) hydrogen bonds : bond 0.07946 ( 587) hydrogen bonds : angle 5.82142 ( 1475) covalent geometry : bond 0.00426 (14418) covalent geometry : angle 0.64174 (20067) *********************** 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 103 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9592 (t80) cc_final: 0.9208 (t80) REVERT: A 96 CYS cc_start: 0.9800 (t) cc_final: 0.9465 (t) REVERT: A 97 GLU cc_start: 0.9779 (mt-10) cc_final: 0.9499 (mm-30) REVERT: B 68 ASP cc_start: 0.8898 (p0) cc_final: 0.8598 (p0) REVERT: B 72 TYR cc_start: 0.8639 (m-80) cc_final: 0.8332 (m-10) REVERT: D 59 MET cc_start: 0.9530 (ttm) cc_final: 0.9222 (mtt) REVERT: E 93 GLN cc_start: 0.9765 (tt0) cc_final: 0.9239 (tt0) REVERT: E 94 GLU cc_start: 0.9782 (tp30) cc_final: 0.9511 (tt0) REVERT: H 253 MET cc_start: 0.9011 (mmp) cc_final: 0.8229 (mtt) REVERT: H 289 MET cc_start: 0.8924 (mpp) cc_final: 0.8471 (mpp) REVERT: H 313 MET cc_start: 0.9304 (ttm) cc_final: 0.8821 (mtp) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2572 time to fit residues: 39.7217 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 : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.020215 restraints weight = 359252.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.021533 restraints weight = 158997.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.022472 restraints weight = 94879.948| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14421 Z= 0.201 Angle : 0.644 8.662 20076 Z= 0.364 Chirality : 0.041 0.196 2249 Planarity : 0.005 0.058 2061 Dihedral : 27.063 139.763 3072 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1292 helix: 0.47 (0.23), residues: 479 sheet: -2.45 (0.37), residues: 159 loop : -1.86 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 922 HIS 0.007 0.001 HIS H 224 PHE 0.014 0.002 PHE H 150 TYR 0.026 0.002 TYR B 88 ARG 0.010 0.001 ARG C 35 Details of bonding type rmsd link_TRANS : bond 0.00169 ( 3) link_TRANS : angle 0.55699 ( 9) hydrogen bonds : bond 0.07910 ( 587) hydrogen bonds : angle 5.76556 ( 1475) covalent geometry : bond 0.00420 (14418) covalent geometry : angle 0.64384 (20067) *********************** 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 103 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9560 (t80) cc_final: 0.9165 (t80) REVERT: A 96 CYS cc_start: 0.9807 (t) cc_final: 0.9419 (t) REVERT: A 97 GLU cc_start: 0.9794 (mt-10) cc_final: 0.9500 (mm-30) REVERT: B 68 ASP cc_start: 0.8908 (p0) cc_final: 0.8616 (p0) REVERT: B 72 TYR cc_start: 0.8608 (m-80) cc_final: 0.8329 (m-10) REVERT: D 59 MET cc_start: 0.9531 (ttm) cc_final: 0.9230 (mtt) REVERT: D 65 PHE cc_start: 0.9779 (t80) cc_final: 0.9570 (t80) REVERT: E 93 GLN cc_start: 0.9760 (tt0) cc_final: 0.9234 (tt0) REVERT: E 94 GLU cc_start: 0.9780 (tp30) cc_final: 0.9395 (tt0) REVERT: G 559 MET cc_start: 0.9013 (tmm) cc_final: 0.8468 (tmm) REVERT: H 253 MET cc_start: 0.8997 (mmp) cc_final: 0.8263 (mtt) REVERT: H 289 MET cc_start: 0.8879 (mpp) cc_final: 0.8636 (mpp) REVERT: H 313 MET cc_start: 0.9293 (ttm) cc_final: 0.8816 (mtp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3441 time to fit residues: 54.1330 Evaluate side-chains 74 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.031865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.019994 restraints weight = 399692.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021370 restraints weight = 168969.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.022336 restraints weight = 98371.743| |-----------------------------------------------------------------------------| r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14421 Z= 0.193 Angle : 0.633 8.114 20076 Z= 0.359 Chirality : 0.041 0.195 2249 Planarity : 0.005 0.062 2061 Dihedral : 27.151 139.026 3072 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1292 helix: 0.57 (0.23), residues: 479 sheet: -2.39 (0.38), residues: 157 loop : -1.83 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 922 HIS 0.007 0.001 HIS H 224 PHE 0.013 0.002 PHE H 403 TYR 0.023 0.002 TYR B 88 ARG 0.006 0.001 ARG C 35 Details of bonding type rmsd link_TRANS : bond 0.00169 ( 3) link_TRANS : angle 0.57045 ( 9) hydrogen bonds : bond 0.07782 ( 587) hydrogen bonds : angle 5.68652 ( 1475) covalent geometry : bond 0.00403 (14418) covalent geometry : angle 0.63352 (20067) *********************** 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 102 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9519 (t80) cc_final: 0.9136 (t80) REVERT: A 96 CYS cc_start: 0.9915 (t) cc_final: 0.9713 (t) REVERT: A 97 GLU cc_start: 0.9874 (mt-10) cc_final: 0.9600 (mm-30) REVERT: B 68 ASP cc_start: 0.8854 (p0) cc_final: 0.8621 (p0) REVERT: D 59 MET cc_start: 0.9626 (ttm) cc_final: 0.9224 (mtt) REVERT: E 93 GLN cc_start: 0.9687 (tt0) cc_final: 0.9266 (tt0) REVERT: E 94 GLU cc_start: 0.9805 (tp30) cc_final: 0.9510 (tt0) REVERT: F 84 MET cc_start: 0.9698 (mpp) cc_final: 0.9444 (mpp) REVERT: G 559 MET cc_start: 0.8626 (tmm) cc_final: 0.8316 (tmm) REVERT: H 253 MET cc_start: 0.9020 (mmp) cc_final: 0.8380 (mtt) REVERT: H 313 MET cc_start: 0.9284 (ttm) cc_final: 0.8830 (mtp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2777 time to fit residues: 42.6521 Evaluate side-chains 71 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 102 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.021478 restraints weight = 395641.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.023026 restraints weight = 159580.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.024128 restraints weight = 91536.333| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14421 Z= 0.127 Angle : 0.599 8.744 20076 Z= 0.337 Chirality : 0.041 0.265 2249 Planarity : 0.004 0.061 2061 Dihedral : 26.898 136.599 3072 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1292 helix: 0.97 (0.24), residues: 474 sheet: -2.03 (0.39), residues: 168 loop : -1.69 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 922 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE H 121 TYR 0.029 0.001 TYR B 88 ARG 0.010 0.001 ARG B 39 Details of bonding type rmsd link_TRANS : bond 0.00165 ( 3) link_TRANS : angle 0.59117 ( 9) hydrogen bonds : bond 0.07978 ( 587) hydrogen bonds : angle 5.13545 ( 1475) covalent geometry : bond 0.00272 (14418) covalent geometry : angle 0.59937 (20067) *********************** 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 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9567 (t80) cc_final: 0.9217 (t80) REVERT: A 96 CYS cc_start: 0.9770 (t) cc_final: 0.9537 (p) REVERT: A 97 GLU cc_start: 0.9700 (mt-10) cc_final: 0.9470 (mm-30) REVERT: B 68 ASP cc_start: 0.8896 (p0) cc_final: 0.8689 (p0) REVERT: B 72 TYR cc_start: 0.8830 (m-10) cc_final: 0.8574 (m-10) REVERT: D 54 ILE cc_start: 0.9616 (mp) cc_final: 0.9246 (tp) REVERT: D 59 MET cc_start: 0.9549 (ttm) cc_final: 0.9096 (mtp) REVERT: D 82 HIS cc_start: 0.9339 (m90) cc_final: 0.9129 (m90) REVERT: E 81 ASP cc_start: 0.9427 (m-30) cc_final: 0.8621 (t0) REVERT: E 89 VAL cc_start: 0.9837 (t) cc_final: 0.9625 (p) REVERT: E 90 MET cc_start: 0.9537 (mmp) cc_final: 0.9285 (mmm) REVERT: E 93 GLN cc_start: 0.9749 (tt0) cc_final: 0.9359 (tp40) REVERT: E 94 GLU cc_start: 0.9781 (tp30) cc_final: 0.9434 (tt0) REVERT: F 62 LEU cc_start: 0.9813 (mt) cc_final: 0.9601 (mt) REVERT: F 84 MET cc_start: 0.9525 (mpp) cc_final: 0.9294 (mpp) REVERT: G 559 MET cc_start: 0.9029 (tmm) cc_final: 0.8608 (tmm) REVERT: H 253 MET cc_start: 0.8907 (mmp) cc_final: 0.8166 (mtt) REVERT: H 289 MET cc_start: 0.8799 (mpp) cc_final: 0.8369 (mpp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2860 time to fit residues: 46.9982 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 : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 77 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.032160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.019627 restraints weight = 409967.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.020952 restraints weight = 186120.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.021889 restraints weight = 112847.269| |-----------------------------------------------------------------------------| r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2442 r_free = 0.2442 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2442 r_free = 0.2442 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14421 Z= 0.192 Angle : 0.641 13.241 20076 Z= 0.361 Chirality : 0.041 0.192 2249 Planarity : 0.005 0.058 2061 Dihedral : 26.955 137.810 3072 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1292 helix: 0.72 (0.24), residues: 477 sheet: -2.07 (0.38), residues: 168 loop : -1.74 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 922 HIS 0.006 0.001 HIS H 224 PHE 0.018 0.002 PHE B 61 TYR 0.021 0.002 TYR B 88 ARG 0.007 0.001 ARG G 569 Details of bonding type rmsd link_TRANS : bond 0.00156 ( 3) link_TRANS : angle 0.57597 ( 9) hydrogen bonds : bond 0.07734 ( 587) hydrogen bonds : angle 5.37985 ( 1475) covalent geometry : bond 0.00408 (14418) covalent geometry : angle 0.64103 (20067) ********************** 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 96 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9539 (t80) cc_final: 0.9191 (t80) REVERT: A 96 CYS cc_start: 0.9892 (t) cc_final: 0.9638 (t) REVERT: A 97 GLU cc_start: 0.9831 (mt-10) cc_final: 0.9572 (mm-30) REVERT: B 72 TYR cc_start: 0.8784 (m-10) cc_final: 0.8572 (m-10) REVERT: D 54 ILE cc_start: 0.9717 (mp) cc_final: 0.9338 (tp) REVERT: D 59 MET cc_start: 0.9606 (ttm) cc_final: 0.9109 (mtm) REVERT: D 82 HIS cc_start: 0.9401 (m90) cc_final: 0.9186 (m-70) REVERT: E 93 GLN cc_start: 0.9660 (tt0) cc_final: 0.9271 (tt0) REVERT: E 94 GLU cc_start: 0.9797 (tp30) cc_final: 0.9490 (tt0) REVERT: F 84 MET cc_start: 0.9721 (mpp) cc_final: 0.9429 (mpp) REVERT: G 559 MET cc_start: 0.8840 (tmm) cc_final: 0.8571 (tmm) REVERT: H 162 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9072 (tp30) REVERT: H 253 MET cc_start: 0.9024 (mmp) cc_final: 0.8367 (mtt) REVERT: H 289 MET cc_start: 0.8719 (mpp) cc_final: 0.8308 (mpp) REVERT: H 313 MET cc_start: 0.9284 (ttm) cc_final: 0.8904 (mtp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2422 time to fit residues: 35.7197 Evaluate side-chains 75 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 89 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 65 optimal weight: 50.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.031575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.019868 restraints weight = 408586.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021256 restraints weight = 168631.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.022233 restraints weight = 97732.468| |-----------------------------------------------------------------------------| r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14421 Z= 0.217 Angle : 0.665 10.971 20076 Z= 0.374 Chirality : 0.041 0.203 2249 Planarity : 0.005 0.058 2061 Dihedral : 27.205 138.712 3072 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1292 helix: 0.48 (0.23), residues: 475 sheet: -2.15 (0.38), residues: 167 loop : -1.74 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 922 HIS 0.008 0.001 HIS H 224 PHE 0.015 0.002 PHE H 403 TYR 0.019 0.002 TYR B 88 ARG 0.012 0.001 ARG B 39 Details of bonding type rmsd link_TRANS : bond 0.00175 ( 3) link_TRANS : angle 0.55772 ( 9) hydrogen bonds : bond 0.07956 ( 587) hydrogen bonds : angle 5.62322 ( 1475) covalent geometry : bond 0.00456 (14418) covalent geometry : angle 0.66499 (20067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5379.75 seconds wall clock time: 100 minutes 23.66 seconds (6023.66 seconds total)