Starting phenix.real_space_refine on Thu Sep 26 19:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_20840.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_20840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_20840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_20840.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/09_2024/6upk_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.22, per 1000 atoms: 0.67 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: 3.43 Conformation dependent library (CDL) restraints added in 1.9 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: 5.78 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: 6.30 Time building geometry restraints manager: 4.01 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: 0.370 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 40.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- 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 14418 Z= 0.343 Angle : 0.939 11.256 20067 Z= 0.554 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.358 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: 0.3130 time to fit residues: 59.0139 Evaluate side-chains 91 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 14418 Z= 0.301 Angle : 0.723 11.466 20067 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.237 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: 0.9420 (t80) cc_final: 0.8921 (t80) REVERT: A 110 CYS cc_start: 0.9159 (m) cc_final: 0.8694 (m) REVERT: B 63 GLU cc_start: 0.9346 (pt0) cc_final: 0.9070 (pt0) REVERT: B 68 ASP cc_start: 0.8725 (p0) cc_final: 0.8305 (p0) REVERT: D 82 HIS cc_start: 0.9830 (t-90) cc_final: 0.9619 (m90) REVERT: E 62 ILE cc_start: 0.9307 (mm) cc_final: 0.9019 (mm) REVERT: E 67 PHE cc_start: 0.9389 (t80) cc_final: 0.8557 (t80) REVERT: E 93 GLN cc_start: 0.9703 (tt0) cc_final: 0.9252 (tp40) REVERT: E 94 GLU cc_start: 0.9790 (tp30) cc_final: 0.9574 (tt0) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.3080 time to fit residues: 51.1724 Evaluate side-chains 84 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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 38 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14418 Z= 0.430 Angle : 0.842 12.796 20067 Z= 0.469 Chirality : 0.047 0.257 2249 Planarity : 0.007 0.068 2061 Dihedral : 27.049 143.669 3072 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 37.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.43 % Allowed : 3.30 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.66 (0.22), residues: 1292 helix: -0.71 (0.22), residues: 477 sheet: -2.80 (0.36), residues: 169 loop : -2.30 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 902 HIS 0.012 0.003 HIS H 224 PHE 0.021 0.003 PHE H 165 TYR 0.028 0.003 TYR H 401 ARG 0.011 0.001 ARG G 569 *********************** 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 100 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.259 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 99 TYR cc_start: 0.9492 (t80) cc_final: 0.8957 (t80) REVERT: A 129 ARG cc_start: 0.9814 (mtt180) cc_final: 0.9537 (mmt180) REVERT: C 50 TYR cc_start: 0.9578 (t80) cc_final: 0.9043 (t80) REVERT: D 82 HIS cc_start: 0.9773 (t-90) cc_final: 0.9566 (m90) REVERT: E 93 GLN cc_start: 0.9762 (tt0) cc_final: 0.9449 (tt0) REVERT: F 84 MET cc_start: 0.9769 (mpp) cc_final: 0.9502 (mpp) REVERT: H 253 MET cc_start: 0.9005 (tpt) cc_final: 0.8778 (tpp) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.2790 time to fit residues: 40.4288 Evaluate side-chains 72 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.0570 chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 50.0000 chunk 132 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- 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** H 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14418 Z= 0.246 Angle : 0.665 10.351 20067 Z= 0.376 Chirality : 0.042 0.242 2249 Planarity : 0.005 0.067 2061 Dihedral : 27.091 141.126 3072 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.18 (0.22), residues: 1292 helix: -0.13 (0.23), residues: 486 sheet: -2.80 (0.35), residues: 176 loop : -2.09 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 922 HIS 0.007 0.001 HIS H 224 PHE 0.015 0.002 PHE H 403 TYR 0.022 0.002 TYR B 88 ARG 0.007 0.001 ARG G 569 *********************** 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 103 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.369 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 99 TYR cc_start: 0.9531 (t80) cc_final: 0.9045 (t80) REVERT: D 59 MET cc_start: 0.9609 (ttm) cc_final: 0.9252 (mtp) REVERT: D 102 LEU cc_start: 0.9411 (tp) cc_final: 0.9206 (tp) REVERT: E 93 GLN cc_start: 0.9740 (tt0) cc_final: 0.9388 (tt0) REVERT: E 94 GLU cc_start: 0.9713 (tt0) cc_final: 0.9321 (tm-30) REVERT: F 84 MET cc_start: 0.9721 (mpp) cc_final: 0.9447 (mpp) REVERT: F 97 LEU cc_start: 0.9544 (mt) cc_final: 0.8975 (mt) REVERT: H 253 MET cc_start: 0.9078 (tpt) cc_final: 0.8288 (ptp) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2624 time to fit residues: 39.9458 Evaluate side-chains 76 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 0.0020 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14418 Z= 0.270 Angle : 0.672 9.444 20067 Z= 0.380 Chirality : 0.042 0.210 2249 Planarity : 0.005 0.066 2061 Dihedral : 27.104 141.093 3072 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.22), residues: 1292 helix: -0.13 (0.23), residues: 486 sheet: -2.76 (0.34), residues: 180 loop : -1.98 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 922 HIS 0.011 0.002 HIS C 31 PHE 0.017 0.002 PHE H 403 TYR 0.023 0.002 TYR B 88 ARG 0.006 0.001 ARG G 569 *********************** 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 96 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 CYS cc_start: 0.9902 (t) cc_final: 0.9691 (t) REVERT: A 97 GLU cc_start: 0.9871 (mt-10) cc_final: 0.9630 (mm-30) REVERT: A 120 MET cc_start: 0.9530 (tmm) cc_final: 0.9326 (ppp) REVERT: D 59 MET cc_start: 0.9621 (ttm) cc_final: 0.9239 (mtt) REVERT: D 102 LEU cc_start: 0.9399 (tp) cc_final: 0.9176 (tp) REVERT: E 93 GLN cc_start: 0.9683 (tt0) cc_final: 0.9380 (tt0) REVERT: E 94 GLU cc_start: 0.9708 (tt0) cc_final: 0.9348 (tm-30) REVERT: F 84 MET cc_start: 0.9736 (mpp) cc_final: 0.9467 (mpp) REVERT: F 97 LEU cc_start: 0.9538 (mt) cc_final: 0.9059 (mt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2776 time to fit residues: 39.4832 Evaluate side-chains 70 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 H 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14418 Z= 0.158 Angle : 0.591 7.716 20067 Z= 0.333 Chirality : 0.041 0.200 2249 Planarity : 0.005 0.068 2061 Dihedral : 26.735 137.373 3072 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.23), residues: 1292 helix: 0.61 (0.24), residues: 485 sheet: -2.46 (0.36), residues: 179 loop : -1.87 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 922 HIS 0.004 0.001 HIS E 113 PHE 0.013 0.001 PHE H 121 TYR 0.024 0.002 TYR B 72 ARG 0.005 0.000 ARG C 35 *********************** 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 121 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.353 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: 0.9579 (t80) cc_final: 0.9236 (t80) REVERT: A 120 MET cc_start: 0.9622 (tmm) cc_final: 0.9357 (tmm) REVERT: A 122 LYS cc_start: 0.9608 (ttpt) cc_final: 0.9400 (pttt) REVERT: B 72 TYR cc_start: 0.9052 (m-80) cc_final: 0.8672 (m-10) REVERT: D 54 ILE cc_start: 0.9686 (mp) cc_final: 0.9212 (tp) REVERT: D 59 MET cc_start: 0.9623 (ttm) cc_final: 0.9137 (mtp) REVERT: D 102 LEU cc_start: 0.9416 (tp) cc_final: 0.9190 (tp) REVERT: E 67 PHE cc_start: 0.9250 (t80) cc_final: 0.8501 (t80) REVERT: E 89 VAL cc_start: 0.9865 (t) cc_final: 0.9572 (p) REVERT: E 90 MET cc_start: 0.9491 (mmp) cc_final: 0.9195 (mmm) REVERT: E 93 GLN cc_start: 0.9710 (tt0) cc_final: 0.9485 (tt0) REVERT: E 94 GLU cc_start: 0.9730 (tt0) cc_final: 0.9277 (tm-30) REVERT: F 84 MET cc_start: 0.9686 (mpp) cc_final: 0.9437 (mpp) REVERT: F 97 LEU cc_start: 0.9504 (mt) cc_final: 0.8904 (mt) REVERT: G 559 MET cc_start: 0.9081 (tmm) cc_final: 0.8689 (tmm) REVERT: H 253 MET cc_start: 0.8904 (tpt) cc_final: 0.8561 (tpp) REVERT: H 313 MET cc_start: 0.9301 (ttm) cc_final: 0.8889 (mtp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2952 time to fit residues: 53.0599 Evaluate side-chains 82 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.0050 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- 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** D 82 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14418 Z= 0.284 Angle : 0.689 11.351 20067 Z= 0.388 Chirality : 0.042 0.201 2249 Planarity : 0.005 0.061 2061 Dihedral : 26.941 139.966 3072 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.71 (0.23), residues: 1292 helix: 0.32 (0.23), residues: 475 sheet: -2.49 (0.36), residues: 174 loop : -1.87 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 922 HIS 0.008 0.001 HIS H 224 PHE 0.017 0.002 PHE H 403 TYR 0.024 0.002 TYR B 72 ARG 0.007 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.315 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: 0.9554 (t80) cc_final: 0.9196 (t80) REVERT: A 120 MET cc_start: 0.9672 (tmm) cc_final: 0.9452 (tmm) REVERT: B 72 TYR cc_start: 0.9107 (m-80) cc_final: 0.8797 (m-10) REVERT: D 91 SER cc_start: 0.9318 (p) cc_final: 0.9046 (m) REVERT: E 93 GLN cc_start: 0.9682 (tt0) cc_final: 0.9394 (tt0) REVERT: E 94 GLU cc_start: 0.9716 (tt0) cc_final: 0.9358 (tm-30) REVERT: F 84 MET cc_start: 0.9718 (mpp) cc_final: 0.9416 (mpp) REVERT: F 97 LEU cc_start: 0.9587 (mt) cc_final: 0.9083 (mt) REVERT: G 540 MET cc_start: 0.7628 (mmm) cc_final: 0.7181 (mmp) REVERT: H 253 MET cc_start: 0.8977 (tpt) cc_final: 0.8059 (ptp) REVERT: H 313 MET cc_start: 0.9365 (ttm) cc_final: 0.9064 (mtp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2596 time to fit residues: 39.1098 Evaluate side-chains 72 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 chunk 95 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** G 550 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14418 Z= 0.162 Angle : 0.601 7.658 20067 Z= 0.340 Chirality : 0.041 0.198 2249 Planarity : 0.004 0.066 2061 Dihedral : 26.773 137.042 3072 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -1.32 (0.23), residues: 1292 helix: 0.71 (0.24), residues: 473 sheet: -2.18 (0.38), residues: 170 loop : -1.74 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 922 HIS 0.003 0.001 HIS B 75 PHE 0.014 0.001 PHE F 61 TYR 0.022 0.001 TYR B 72 ARG 0.005 0.000 ARG G 569 *********************** 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 108 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.466 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: 0.9532 (t80) cc_final: 0.9191 (t80) REVERT: A 110 CYS cc_start: 0.9260 (m) cc_final: 0.9032 (m) REVERT: A 120 MET cc_start: 0.9753 (tmm) cc_final: 0.9547 (tmm) REVERT: B 72 TYR cc_start: 0.9137 (m-80) cc_final: 0.8804 (m-10) REVERT: D 54 ILE cc_start: 0.9722 (mp) cc_final: 0.9281 (tp) REVERT: D 59 MET cc_start: 0.9617 (ttm) cc_final: 0.9078 (mtp) REVERT: D 102 LEU cc_start: 0.9410 (tp) cc_final: 0.9206 (tp) REVERT: E 67 PHE cc_start: 0.9159 (t80) cc_final: 0.8538 (t80) REVERT: E 81 ASP cc_start: 0.9296 (m-30) cc_final: 0.8657 (t0) REVERT: E 89 VAL cc_start: 0.9872 (t) cc_final: 0.9568 (p) REVERT: E 90 MET cc_start: 0.9490 (mmp) cc_final: 0.9178 (mmm) REVERT: E 93 GLN cc_start: 0.9629 (tt0) cc_final: 0.9384 (tt0) REVERT: E 94 GLU cc_start: 0.9710 (tt0) cc_final: 0.9286 (tm-30) REVERT: F 84 MET cc_start: 0.9691 (mpp) cc_final: 0.9483 (mpp) REVERT: F 97 LEU cc_start: 0.9525 (mt) cc_final: 0.9020 (mt) REVERT: G 559 MET cc_start: 0.9023 (tmm) cc_final: 0.8625 (tmm) REVERT: H 253 MET cc_start: 0.9045 (tpt) cc_final: 0.8297 (ptp) REVERT: H 289 MET cc_start: 0.8758 (mpp) cc_final: 0.8465 (mpp) REVERT: H 313 MET cc_start: 0.9286 (ttm) cc_final: 0.8885 (mtp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2661 time to fit residues: 42.7802 Evaluate side-chains 74 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- 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** G 550 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14418 Z= 0.174 Angle : 0.594 7.500 20067 Z= 0.337 Chirality : 0.040 0.194 2249 Planarity : 0.005 0.059 2061 Dihedral : 26.716 138.070 3072 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.74 (0.24), residues: 476 sheet: -2.10 (0.38), residues: 169 loop : -1.74 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 922 HIS 0.005 0.001 HIS H 224 PHE 0.011 0.001 PHE H 121 TYR 0.021 0.002 TYR B 72 ARG 0.010 0.000 ARG B 39 *********************** 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 104 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.411 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: 0.9447 (t80) cc_final: 0.9081 (t80) REVERT: A 110 CYS cc_start: 0.9306 (m) cc_final: 0.9083 (m) REVERT: B 72 TYR cc_start: 0.9186 (m-80) cc_final: 0.8840 (m-10) REVERT: D 54 ILE cc_start: 0.9737 (mp) cc_final: 0.9373 (tp) REVERT: D 59 MET cc_start: 0.9612 (ttm) cc_final: 0.9079 (mtp) REVERT: E 67 PHE cc_start: 0.9148 (t80) cc_final: 0.8547 (t80) REVERT: E 81 ASP cc_start: 0.9304 (m-30) cc_final: 0.8670 (t0) REVERT: E 93 GLN cc_start: 0.9626 (tt0) cc_final: 0.9392 (tt0) REVERT: E 94 GLU cc_start: 0.9703 (tt0) cc_final: 0.9306 (tm-30) REVERT: F 97 LEU cc_start: 0.9570 (mt) cc_final: 0.9123 (mt) REVERT: G 559 MET cc_start: 0.9018 (tmm) cc_final: 0.8616 (tmm) REVERT: H 253 MET cc_start: 0.9054 (tpt) cc_final: 0.8290 (ptp) REVERT: H 289 MET cc_start: 0.8777 (mpp) cc_final: 0.8488 (mpp) REVERT: H 313 MET cc_start: 0.9311 (ttm) cc_final: 0.8871 (mtp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2710 time to fit residues: 41.3681 Evaluate side-chains 72 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 50.0000 chunk 95 optimal weight: 0.0270 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 overall best weight: 6.0046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14418 Z= 0.328 Angle : 0.721 8.217 20067 Z= 0.407 Chirality : 0.043 0.197 2249 Planarity : 0.006 0.059 2061 Dihedral : 27.132 139.837 3072 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 30.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.22), residues: 1292 helix: 0.26 (0.23), residues: 475 sheet: -2.32 (0.37), residues: 163 loop : -1.85 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 902 HIS 0.010 0.002 HIS H 224 PHE 0.022 0.002 PHE H 150 TYR 0.021 0.002 TYR H 401 ARG 0.007 0.001 ARG B 45 ********************** 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 85 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.9106 (m-80) cc_final: 0.8848 (m-10) REVERT: D 59 MET cc_start: 0.9621 (ttm) cc_final: 0.9221 (mtt) REVERT: D 102 LEU cc_start: 0.9437 (tp) cc_final: 0.9233 (tp) REVERT: E 93 GLN cc_start: 0.9633 (tt0) cc_final: 0.9354 (tt0) REVERT: E 94 GLU cc_start: 0.9705 (tt0) cc_final: 0.9378 (tm-30) REVERT: F 97 LEU cc_start: 0.9605 (mt) cc_final: 0.9207 (mt) REVERT: G 540 MET cc_start: 0.7330 (mmm) cc_final: 0.6987 (mmt) REVERT: H 253 MET cc_start: 0.9090 (tpt) cc_final: 0.8841 (tpp) REVERT: H 313 MET cc_start: 0.9339 (ttm) cc_final: 0.8949 (mtp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2755 time to fit residues: 34.9513 Evaluate side-chains 59 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 30.0000 chunk 35 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.2844 r_free = 0.2844 target = 0.033484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.021118 restraints weight = 414568.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.022601 restraints weight = 170507.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.023632 restraints weight = 98711.038| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14418 Z= 0.172 Angle : 0.614 7.521 20067 Z= 0.347 Chirality : 0.041 0.194 2249 Planarity : 0.004 0.065 2061 Dihedral : 26.955 137.331 3072 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.32 (0.23), residues: 1292 helix: 0.66 (0.24), residues: 479 sheet: -2.12 (0.38), residues: 168 loop : -1.73 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 922 HIS 0.004 0.001 HIS H 224 PHE 0.012 0.001 PHE H 121 TYR 0.021 0.002 TYR B 72 ARG 0.007 0.000 ARG F 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.06 seconds wall clock time: 41 minutes 24.04 seconds (2484.04 seconds total)