Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:46:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/12_2022/6ahr_9626_neut.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 831": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B ARG 1008": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 27851 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 7295 Classifications: {'RNA': 341} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 19, 'rna3p_pur': 153, 'rna3p_pyr': 142} Link IDs: {'rna2p': 46, 'rna3p': 294} Chain: "B" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6142 Classifications: {'peptide': 774} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 723} Chain breaks: 4 Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1448 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1197 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 10, 'TRANS': 118} Chain breaks: 2 Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1021 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1824 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "J" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1905 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "K" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 979 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 341} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24422 SG CYS K 62 59.158 83.678 50.866 1.00111.85 S ATOM 24659 SG CYS K 92 57.012 80.753 51.196 1.00115.22 S Time building chain proxies: 16.01, per 1000 atoms: 0.57 Number of scatterers: 27851 At special positions: 0 Unit cell: (143.88, 134.64, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 112 16.00 P 341 15.00 O 6076 8.00 N 4995 7.00 C 16326 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.66 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 92 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 62 " 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 40.2% alpha, 17.9% beta 86 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 8.40 Creating SS restraints... Processing helix chain 'B' and resid 100 through 127 removed outlier: 3.642A pdb=" N ALA B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 4.061A pdb=" N ARG B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.818A pdb=" N MET B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 145' Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.029A pdb=" N ARG B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 4.117A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.806A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.721A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 removed outlier: 4.024A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.519A pdb=" N LYS B 287 " --> pdb=" O CYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 4.301A pdb=" N GLU B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.692A pdb=" N HIS B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.881A pdb=" N ASP B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 473 through 493 removed outlier: 4.327A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.665A pdb=" N VAL B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.590A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 643 through 654 removed outlier: 3.549A pdb=" N LYS B 654 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 Processing helix chain 'B' and resid 707 through 722 removed outlier: 4.097A pdb=" N GLN B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 820 removed outlier: 3.568A pdb=" N TRP B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 removed outlier: 3.526A pdb=" N CYS B 845 " --> pdb=" O THR B 841 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 849 " --> pdb=" O CYS B 845 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.640A pdb=" N ASP B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 920 removed outlier: 3.995A pdb=" N LYS B 907 " --> pdb=" O PRO B 903 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 920 " --> pdb=" O LYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 957 removed outlier: 4.361A pdb=" N ARG B 954 " --> pdb=" O GLY B 950 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 955 " --> pdb=" O PRO B 951 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 957' Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.542A pdb=" N LEU B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 992 " --> pdb=" O THR B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 removed outlier: 3.612A pdb=" N GLN C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 removed outlier: 3.586A pdb=" N GLU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.565A pdb=" N ARG C 110 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 111 " --> pdb=" O HIS C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.434A pdb=" N ARG C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.435A pdb=" N LEU C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.603A pdb=" N ARG C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.872A pdb=" N GLN D 93 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 94 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 115 removed outlier: 4.078A pdb=" N HIS D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.951A pdb=" N SER D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 106 through 130 removed outlier: 4.040A pdb=" N LEU E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 148 removed outlier: 4.074A pdb=" N ALA E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.024A pdb=" N PHE F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 59 removed outlier: 4.071A pdb=" N ARG F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 88 removed outlier: 3.768A pdb=" N ALA F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.512A pdb=" N SER G 28 " --> pdb=" O ARG G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.879A pdb=" N GLN G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 93 removed outlier: 3.945A pdb=" N ALA G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE G 93 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.618A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 50 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 91 Processing helix chain 'H' and resid 112 through 117 removed outlier: 3.960A pdb=" N ASN H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.584A pdb=" N ILE I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 180 Processing helix chain 'I' and resid 201 through 211 removed outlier: 3.944A pdb=" N ASN I 205 " --> pdb=" O TYR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 237 removed outlier: 4.593A pdb=" N ARG I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 83 through 93 Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.694A pdb=" N ILE J 142 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 180 Processing helix chain 'J' and resid 202 through 211 removed outlier: 3.635A pdb=" N PHE J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 237 removed outlier: 4.257A pdb=" N ARG J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 28 removed outlier: 3.727A pdb=" N GLN K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 61 Processing helix chain 'K' and resid 69 through 74 removed outlier: 4.160A pdb=" N LEU K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 106 No H-bonds generated for 'chain 'K' and resid 104 through 106' Processing helix chain 'K' and resid 107 through 113 Processing helix chain 'K' and resid 114 through 121 removed outlier: 4.412A pdb=" N LEU K 118 " --> pdb=" O PRO K 114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY K 119 " --> pdb=" O GLU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 28 through 35 Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.509A pdb=" N LEU L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 120 through 128 removed outlier: 3.509A pdb=" N GLY L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.748A pdb=" N LEU L 155 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.503A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 197 removed outlier: 3.816A pdb=" N TYR L 196 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 248 Processing helix chain 'L' and resid 286 through 300 Processing helix chain 'L' and resid 301 through 303 No H-bonds generated for 'chain 'L' and resid 301 through 303' Processing sheet with id=AA1, first strand: chain 'B' and resid 212 through 216 removed outlier: 7.039A pdb=" N HIS B 213 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 448 through 449 removed outlier: 4.174A pdb=" N LYS B 448 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 595 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 295 removed outlier: 3.558A pdb=" N GLY B 306 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 313 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 326 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 257 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.440A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 978 " --> pdb=" O SER B 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.440A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 965 " --> pdb=" O ILE B 875 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 982 " --> pdb=" O THR B 968 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 978 " --> pdb=" O SER B 973 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 115 removed outlier: 3.804A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 174 through 178 removed outlier: 6.052A pdb=" N ILE D 139 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 187 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 183 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 192 " --> pdb=" O THR J 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 58 removed outlier: 6.726A pdb=" N VAL E 55 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG E 68 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR E 8 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS E 102 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU E 10 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 100 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 2 through 7 removed outlier: 6.836A pdb=" N MET F 38 " --> pdb=" O CYS F 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 18 through 21 removed outlier: 3.828A pdb=" N GLU G 19 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL G 108 " --> pdb=" O GLU G 19 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N THR G 21 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU G 106 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN G 35 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS G 72 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.993A pdb=" N GLU H 9 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS L 19 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU L 14 " --> pdb=" O VAL L 355 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 67 removed outlier: 6.050A pdb=" N ILE H 63 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG H 76 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR H 65 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE H 74 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 72 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS H 25 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL H 104 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU H 27 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE H 102 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.858A pdb=" N LEU I 7 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 38 through 39 removed outlier: 6.643A pdb=" N VAL I 39 " --> pdb=" O ILE I 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 152 through 156 Processing sheet with id=AB8, first strand: chain 'J' and resid 6 through 9 removed outlier: 4.167A pdb=" N LEU J 7 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 34 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL J 33 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 38 through 39 removed outlier: 6.650A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 76 through 81 Processing sheet with id=AC3, first strand: chain 'L' and resid 132 through 136 removed outlier: 6.482A pdb=" N ILE L 145 " --> pdb=" O PRO L 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL L 107 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE L 179 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS L 70 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU L 181 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE L 68 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N TRP L 183 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N TYR L 66 " --> pdb=" O TRP L 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 322 through 323 857 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 232 hydrogen bonds 444 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 12.24 Time building geometry restraints manager: 12.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6657 1.34 - 1.46: 7548 1.46 - 1.58: 14099 1.58 - 1.70: 681 1.70 - 1.82: 147 Bond restraints: 29132 Sorted by residual: bond pdb=" C CYS B 706 " pdb=" N PRO B 707 " ideal model delta sigma weight residual 1.332 1.384 -0.052 8.20e-03 1.49e+04 4.06e+01 bond pdb=" C ILE B 632 " pdb=" N PRO B 633 " ideal model delta sigma weight residual 1.336 1.409 -0.074 1.23e-02 6.61e+03 3.58e+01 bond pdb=" C VAL K 70 " pdb=" N PRO K 71 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.19e+01 bond pdb=" C VAL C 161 " pdb=" N PRO C 162 " ideal model delta sigma weight residual 1.336 1.385 -0.049 9.80e-03 1.04e+04 2.53e+01 bond pdb=" C SER I 157 " pdb=" N PRO I 158 " ideal model delta sigma weight residual 1.332 1.366 -0.034 8.20e-03 1.49e+04 1.74e+01 ... (remaining 29127 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.93: 2737 106.93 - 113.80: 16851 113.80 - 120.68: 11696 120.68 - 127.56: 8971 127.56 - 134.43: 827 Bond angle restraints: 41082 Sorted by residual: angle pdb=" C LEU K 69 " pdb=" N VAL K 70 " pdb=" CA VAL K 70 " ideal model delta sigma weight residual 120.33 125.87 -5.54 8.00e-01 1.56e+00 4.80e+01 angle pdb=" C ARG G 23 " pdb=" N LYS G 24 " pdb=" CA LYS G 24 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C LEU C 174 " pdb=" N LYS C 175 " pdb=" CA LYS C 175 " ideal model delta sigma weight residual 120.82 128.50 -7.68 1.47e+00 4.63e-01 2.73e+01 angle pdb=" C CYS I 180 " pdb=" N LYS I 181 " pdb=" CA LYS I 181 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG D 95 " pdb=" N TYR D 96 " pdb=" CA TYR D 96 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 ... (remaining 41077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16585 35.58 - 71.16: 315 71.16 - 106.74: 30 106.74 - 142.32: 1 142.32 - 177.91: 6 Dihedral angle restraints: 16937 sinusoidal: 9386 harmonic: 7551 Sorted by residual: dihedral pdb=" C4' G A 12 " pdb=" C3' G A 12 " pdb=" C2' G A 12 " pdb=" C1' G A 12 " ideal model delta sinusoidal sigma weight residual -35.00 36.14 -71.14 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' U A 80 " pdb=" C3' U A 80 " pdb=" C2' U A 80 " pdb=" C1' U A 80 " ideal model delta sinusoidal sigma weight residual -35.00 36.14 -71.14 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' U A 80 " pdb=" C2' U A 80 " pdb=" C1' U A 80 " pdb=" C3' U A 80 " ideal model delta sinusoidal sigma weight residual -35.00 32.68 -67.68 1 8.00e+00 1.56e-02 9.30e+01 ... (remaining 16934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4381 0.076 - 0.153: 459 0.153 - 0.229: 77 0.229 - 0.306: 4 0.306 - 0.382: 2 Chirality restraints: 4923 Sorted by residual: chirality pdb=" CB ILE B 499 " pdb=" CA ILE B 499 " pdb=" CG1 ILE B 499 " pdb=" CG2 ILE B 499 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C3' G A 261 " pdb=" C4' G A 261 " pdb=" O3' G A 261 " pdb=" C2' G A 261 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CG LEU D 84 " pdb=" CB LEU D 84 " pdb=" CD1 LEU D 84 " pdb=" CD2 LEU D 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4920 not shown) Planarity restraints: 3950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 148 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO F 149 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 61 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO J 62 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO J 62 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 62 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR J 60 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C THR J 60 " -0.048 2.00e-02 2.50e+03 pdb=" O THR J 60 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU J 61 " 0.016 2.00e-02 2.50e+03 ... (remaining 3947 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 36 2.37 - 3.01: 12407 3.01 - 3.64: 41032 3.64 - 4.27: 62527 4.27 - 4.90: 96014 Nonbonded interactions: 212016 Sorted by model distance: nonbonded pdb=" O4' G A 73 " pdb=" N6 A A 315 " model vdw 1.742 2.520 nonbonded pdb=" O2' C A 326 " pdb=" O5' U A 327 " model vdw 1.851 2.440 nonbonded pdb=" O2' G A 12 " pdb=" OP1 G A 13 " model vdw 1.873 2.440 nonbonded pdb=" N6 A A 269 " pdb=" N3 A A 315 " model vdw 1.942 2.600 nonbonded pdb=" OP1 C A 328 " pdb=" NH2 ARG L 139 " model vdw 1.959 2.520 ... (remaining 212011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 237) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 341 5.49 5 S 112 5.16 5 C 16326 2.51 5 N 4995 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.250 Process input model: 81.900 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 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 : 0.004 0.095 29132 Z= 0.255 Angle : 0.956 16.429 41082 Z= 0.547 Chirality : 0.050 0.382 4923 Planarity : 0.007 0.081 3950 Dihedral : 12.845 177.906 12033 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.16 % Favored : 89.57 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.20 % 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: -4.23 (0.13), residues: 2559 helix: -2.76 (0.12), residues: 885 sheet: -1.14 (0.20), residues: 562 loop : -3.75 (0.15), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 973 time to evaluate : 2.659 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: 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 outliers start: 3 outliers final: 2 residues processed: 976 average time/residue: 0.4590 time to fit residues: 654.3525 Evaluate side-chains 464 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 462 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2266 time to fit residues: 4.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 0.7980 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 chunk 147 optimal weight: 0.0570 chunk 117 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 464 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN B 658 ASN B 802 HIS B 872 HIS C 27 ASN C 42 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN E 89 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 107 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 HIS I 175 ASN I 224 ASN K 27 GLN K 103 ASN K 107 HIS L 34 GLN L 62 ASN L 132 HIS L 206 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 223 GLN L 258 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 29132 Z= 0.194 Angle : 0.720 15.469 41082 Z= 0.361 Chirality : 0.040 0.265 4923 Planarity : 0.006 0.061 3950 Dihedral : 13.459 176.177 6920 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.67 % Favored : 89.25 % Rotamer Outliers : 5.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.99 (0.15), residues: 2559 helix: -0.92 (0.16), residues: 914 sheet: -0.93 (0.21), residues: 560 loop : -3.57 (0.16), residues: 1085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 516 time to evaluate : 2.626 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 outliers start: 116 outliers final: 62 residues processed: 593 average time/residue: 0.3933 time to fit residues: 364.2223 Evaluate side-chains 461 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 399 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.2559 time to fit residues: 32.9101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 0.0980 chunk 81 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 284 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 260 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 210 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 HIS B 658 ASN B 891 HIS C 42 HIS ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN H 42 GLN I 86 HIS I 114 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 224 ASN L 62 ASN L 132 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 258 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29132 Z= 0.174 Angle : 0.679 14.009 41082 Z= 0.335 Chirality : 0.039 0.229 4923 Planarity : 0.005 0.053 3950 Dihedral : 13.059 174.429 6920 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.02 % Favored : 88.94 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.49 (0.16), residues: 2559 helix: -0.31 (0.16), residues: 921 sheet: -0.75 (0.22), residues: 545 loop : -3.40 (0.16), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 452 time to evaluate : 2.587 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 outliers start: 62 outliers final: 26 residues processed: 487 average time/residue: 0.3768 time to fit residues: 291.9228 Evaluate side-chains 417 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 391 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2570 time to fit residues: 15.5757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 75 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 160 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN C 26 ASN C 42 HIS ** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN E 102 HIS E 111 GLN E 116 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN H 106 GLN I 114 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.154 29132 Z= 0.344 Angle : 0.858 14.393 41082 Z= 0.428 Chirality : 0.045 0.317 4923 Planarity : 0.007 0.088 3950 Dihedral : 13.512 176.998 6920 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.25 % Favored : 88.63 % Rotamer Outliers : 5.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % 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: -2.53 (0.16), residues: 2559 helix: -0.37 (0.16), residues: 937 sheet: -0.74 (0.22), residues: 529 loop : -3.42 (0.16), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 481 time to evaluate : 2.725 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 outliers start: 125 outliers final: 64 residues processed: 560 average time/residue: 0.3979 time to fit residues: 348.4803 Evaluate side-chains 459 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 395 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 1 residues processed: 64 average time/residue: 0.2656 time to fit residues: 34.6837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS E 41 HIS ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN G 48 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 29132 Z= 0.246 Angle : 0.740 12.578 41082 Z= 0.367 Chirality : 0.042 0.215 4923 Planarity : 0.005 0.058 3950 Dihedral : 13.273 174.909 6920 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.25 % Favored : 88.71 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.04 % 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: -2.43 (0.16), residues: 2559 helix: -0.16 (0.16), residues: 955 sheet: -0.85 (0.22), residues: 533 loop : -3.46 (0.16), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 453 time to evaluate : 2.606 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 outliers start: 69 outliers final: 38 residues processed: 495 average time/residue: 0.3890 time to fit residues: 309.3796 Evaluate side-chains 417 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 379 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2516 time to fit residues: 21.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 279 optimal weight: 0.2980 chunk 232 optimal weight: 0.1980 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 138 HIS ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 42 HIS ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS I 65 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.8185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 29132 Z= 0.209 Angle : 0.721 13.929 41082 Z= 0.353 Chirality : 0.041 0.261 4923 Planarity : 0.006 0.127 3950 Dihedral : 13.157 173.739 6920 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.86 % Favored : 89.10 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.04 % 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: -2.27 (0.16), residues: 2559 helix: -0.05 (0.16), residues: 958 sheet: -0.84 (0.22), residues: 539 loop : -3.33 (0.17), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 429 time to evaluate : 2.658 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 outliers start: 60 outliers final: 36 residues processed: 464 average time/residue: 0.3736 time to fit residues: 276.3439 Evaluate side-chains 426 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 390 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2461 time to fit residues: 19.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.9800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.144 29132 Z= 0.370 Angle : 0.880 13.503 41082 Z= 0.442 Chirality : 0.047 0.339 4923 Planarity : 0.006 0.079 3950 Dihedral : 13.933 174.704 6920 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.78 % Favored : 87.14 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % 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: -2.57 (0.16), residues: 2559 helix: -0.35 (0.16), residues: 940 sheet: -1.03 (0.22), residues: 553 loop : -3.39 (0.17), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 446 time to evaluate : 3.093 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 outliers start: 76 outliers final: 38 residues processed: 488 average time/residue: 0.3879 time to fit residues: 301.3667 Evaluate side-chains 411 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 373 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2744 time to fit residues: 22.3226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 166 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 59 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.9766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 29132 Z= 0.209 Angle : 0.782 14.420 41082 Z= 0.380 Chirality : 0.042 0.296 4923 Planarity : 0.005 0.073 3950 Dihedral : 13.486 173.990 6920 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.90 % Favored : 89.06 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: -2.38 (0.16), residues: 2559 helix: -0.11 (0.17), residues: 961 sheet: -0.96 (0.22), residues: 554 loop : -3.41 (0.17), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 436 time to evaluate : 2.809 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 outliers start: 27 outliers final: 16 residues processed: 446 average time/residue: 0.3835 time to fit residues: 273.6025 Evaluate side-chains 397 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 381 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2837 time to fit residues: 11.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5114 > 50: distance: 4 - 25: 24.186 distance: 20 - 25: 27.990 distance: 25 - 26: 29.731 distance: 26 - 27: 21.158 distance: 26 - 29: 34.045 distance: 27 - 28: 23.562 distance: 27 - 33: 32.588 distance: 29 - 30: 35.808 distance: 30 - 31: 26.154 distance: 31 - 32: 19.716 distance: 33 - 34: 23.030 distance: 34 - 35: 17.671 distance: 34 - 37: 25.789 distance: 35 - 36: 46.381 distance: 35 - 41: 48.975 distance: 37 - 38: 8.115 distance: 38 - 39: 35.451 distance: 41 - 42: 33.699 distance: 42 - 43: 24.897 distance: 43 - 44: 46.371 distance: 43 - 48: 11.390 distance: 48 - 49: 35.233 distance: 49 - 50: 40.180 distance: 50 - 51: 37.863 distance: 50 - 52: 34.449 distance: 52 - 53: 17.266 distance: 52 - 58: 38.955 distance: 53 - 54: 28.565 distance: 53 - 56: 52.583 distance: 54 - 55: 20.129 distance: 54 - 59: 36.272 distance: 56 - 57: 45.905 distance: 57 - 58: 32.565 distance: 59 - 60: 29.154 distance: 59 - 191: 25.684 distance: 60 - 61: 44.395 distance: 60 - 63: 15.105 distance: 61 - 62: 44.454 distance: 61 - 71: 36.849 distance: 62 - 188: 28.760 distance: 63 - 64: 39.801 distance: 64 - 65: 46.648 distance: 64 - 66: 24.404 distance: 65 - 67: 7.036 distance: 66 - 68: 19.314 distance: 67 - 69: 14.026 distance: 68 - 69: 27.410 distance: 69 - 70: 36.127 distance: 71 - 72: 41.979 distance: 72 - 73: 41.724 distance: 72 - 75: 12.990 distance: 73 - 74: 57.915 distance: 73 - 83: 49.015 distance: 75 - 76: 38.359 distance: 76 - 77: 24.664 distance: 76 - 78: 33.718 distance: 77 - 79: 12.653 distance: 78 - 80: 11.619 distance: 79 - 81: 28.454 distance: 80 - 81: 31.581 distance: 81 - 82: 18.039 distance: 83 - 84: 46.608 distance: 83 - 177: 26.204 distance: 84 - 85: 46.154 distance: 84 - 87: 37.533 distance: 85 - 86: 51.116 distance: 85 - 94: 43.473 distance: 86 - 174: 25.657 distance: 87 - 88: 23.021 distance: 88 - 89: 16.608 distance: 88 - 90: 6.481 distance: 89 - 91: 23.996 distance: 90 - 92: 24.761 distance: 91 - 93: 16.175 distance: 92 - 93: 21.074 distance: 94 - 95: 40.382 distance: 95 - 96: 68.511 distance: 95 - 98: 58.632 distance: 96 - 97: 53.483 distance: 96 - 101: 63.670 distance: 98 - 99: 45.790 distance: 98 - 100: 16.734 distance: 101 - 102: 40.903 distance: 102 - 103: 33.484 distance: 102 - 105: 34.677 distance: 103 - 104: 28.325 distance: 103 - 110: 18.518 distance: 105 - 106: 35.460 distance: 106 - 107: 32.401 distance: 107 - 108: 25.415 distance: 108 - 109: 6.631