Starting phenix.real_space_refine (version: dev) on Fri Apr 8 02:51:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/04_2022/6d6r_7809_updated.pdb" } resolution = 3.45 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= 0.004 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 "A ARG 70": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 6": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 407": "NH1" <-> "NH2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "K ARG 557": "NH1" <-> "NH2" Residue "K PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 624": "NH1" <-> "NH2" Residue "K ARG 638": "NH1" <-> "NH2" Residue "K ARG 741": "NH1" <-> "NH2" Residue "K ARG 781": "NH1" <-> "NH2" Residue "K ARG 829": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "M PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M ARG 995": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 31639 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1859 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "I" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 6856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6856 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 40, 'TRANS': 812} Chain breaks: 6 Chain: "L" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 573 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5648 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 683, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'RNA': 35, 'DNA': 13} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 17, 'rna2p_pyr': 5, 'rna3p_pyr': 11} Link IDs: {'rna3p': 41, 'rna2p': 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 1, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' C%rna3p_pyr:plan2': 2, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17538 SG CYS K 31 45.199 135.961 78.802 1.00 75.54 S ATOM 17564 SG CYS K 36 45.007 136.828 82.641 1.00 92.82 S ATOM 17580 SG CYS K 39 43.986 133.311 81.292 1.00 97.97 S Time building chain proxies: 17.35, per 1000 atoms: 0.55 Number of scatterers: 31639 At special positions: 0 Unit cell: (164.78, 191.53, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 196 16.00 P 61 15.00 Mg 1 11.99 O 6074 8.00 N 5611 7.00 C 19695 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: 13.28 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 159 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 31 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 39 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 36 " Number of angles added : 3 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 38 sheets defined 30.3% alpha, 17.4% beta 14 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 10.71 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 244 through 276 removed outlier: 4.055A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.597A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.857A pdb=" N CYS B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 209 through 242 Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.055A pdb=" N PHE C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 121 through 124 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 271 removed outlier: 4.169A pdb=" N GLN C 249 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP C 250 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 130 through 143 removed outlier: 4.147A pdb=" N ASN D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 203 through 231 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 121 through 124 Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 216 through 219 No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 251 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 119 through 130 Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 234 through 269 Proline residue: F 253 - end of helix Processing helix chain 'G' and resid 204 through 210 Processing helix chain 'G' and resid 217 through 224 removed outlier: 3.981A pdb=" N GLY G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 256 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 125 through 133 removed outlier: 4.975A pdb=" N ARG H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 228 through 247 removed outlier: 4.690A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 274 through 292 Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 118 through 121 No H-bonds generated for 'chain 'I' and resid 118 through 121' Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 103 through 113 Processing helix chain 'K' and resid 141 through 163 Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 194 through 200 Processing helix chain 'K' and resid 206 through 209 No H-bonds generated for 'chain 'K' and resid 206 through 209' Processing helix chain 'K' and resid 234 through 243 removed outlier: 3.882A pdb=" N LYS K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 436 removed outlier: 4.640A pdb=" N GLU K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 451 Processing helix chain 'K' and resid 463 through 465 No H-bonds generated for 'chain 'K' and resid 463 through 465' Processing helix chain 'K' and resid 509 through 512 No H-bonds generated for 'chain 'K' and resid 509 through 512' Processing helix chain 'K' and resid 518 through 525 Processing helix chain 'K' and resid 542 through 546 Processing helix chain 'K' and resid 590 through 598 Processing helix chain 'K' and resid 607 through 626 removed outlier: 3.909A pdb=" N LEU K 616 " --> pdb=" O GLY K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 658 through 681 Processing helix chain 'K' and resid 700 through 708 Processing helix chain 'K' and resid 718 through 725 Processing helix chain 'K' and resid 731 through 733 No H-bonds generated for 'chain 'K' and resid 731 through 733' Processing helix chain 'K' and resid 737 through 745 Processing helix chain 'K' and resid 783 through 795 Processing helix chain 'K' and resid 802 through 804 No H-bonds generated for 'chain 'K' and resid 802 through 804' Processing helix chain 'K' and resid 807 through 842 Processing helix chain 'L' and resid 11 through 14 No H-bonds generated for 'chain 'L' and resid 11 through 14' Processing helix chain 'L' and resid 17 through 20 No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 64 through 67 No H-bonds generated for 'chain 'L' and resid 64 through 67' Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'M' and resid 142 through 152 Processing helix chain 'M' and resid 169 through 180 Processing helix chain 'M' and resid 193 through 206 Processing helix chain 'M' and resid 230 through 238 Processing helix chain 'M' and resid 255 through 258 Processing helix chain 'M' and resid 263 through 272 removed outlier: 4.122A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 300 Processing helix chain 'M' and resid 340 through 353 Processing helix chain 'M' and resid 374 through 383 Processing helix chain 'M' and resid 397 through 408 removed outlier: 5.028A pdb=" N LYS M 408 " --> pdb=" O LEU M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 430 removed outlier: 5.006A pdb=" N CYS M 430 " --> pdb=" O ASN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 450 Proline residue: M 446 - end of helix Processing helix chain 'M' and resid 461 through 473 Processing helix chain 'M' and resid 484 through 487 No H-bonds generated for 'chain 'M' and resid 484 through 487' Processing helix chain 'M' and resid 514 through 523 removed outlier: 4.547A pdb=" N ARG M 523 " --> pdb=" O GLN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 552 Processing helix chain 'M' and resid 567 through 574 Processing helix chain 'M' and resid 581 through 587 Processing helix chain 'M' and resid 589 through 594 removed outlier: 4.199A pdb=" N HIS M 594 " --> pdb=" O TYR M 590 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 608 Processing helix chain 'M' and resid 832 through 839 Processing helix chain 'M' and resid 848 through 861 Processing helix chain 'M' and resid 872 through 877 Processing helix chain 'M' and resid 885 through 894 Processing helix chain 'M' and resid 902 through 913 removed outlier: 3.876A pdb=" N THR M 906 " --> pdb=" O ALA M 902 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE M 912 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 948 Proline residue: M 931 - end of helix removed outlier: 3.555A pdb=" N GLN M 934 " --> pdb=" O GLY M 930 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 960 Processing helix chain 'M' and resid 967 through 974 Processing helix chain 'M' and resid 979 through 981 No H-bonds generated for 'chain 'M' and resid 979 through 981' Processing helix chain 'M' and resid 990 through 1014 Processing helix chain 'M' and resid 1018 through 1030 Processing sheet with id= A, first strand: chain 'A' and resid 284 through 286 Processing sheet with id= B, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= C, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.781A pdb=" N MET A 225 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 219 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 233 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 24 through 27 removed outlier: 3.700A pdb=" N GLN B 128 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 48 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL B 126 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 50 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 124 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 52 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE B 122 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 70 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE B 122 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 72 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 124 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 74 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 126 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.174A pdb=" N LEU B 189 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE B 195 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.867A pdb=" N ASP C 143 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 59 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N CYS C 141 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 61 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU C 139 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 63 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N CYS C 137 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU C 65 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU C 135 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 67 " --> pdb=" O TRP C 133 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP C 133 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.862A pdb=" N VAL C 194 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS C 234 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP C 227 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU C 232 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.963A pdb=" N GLU C 167 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS C 183 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 12.524A pdb=" N THR C 169 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N LEU C 181 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N ASN C 171 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N VAL C 179 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.752A pdb=" N SER D 53 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU D 55 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL D 122 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY D 57 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU D 120 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR D 59 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL D 118 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.874A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 35 through 39 removed outlier: 6.891A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 168 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 209 through 211 removed outlier: 4.384A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.814A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 63 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 150 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA F 65 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA F 148 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER F 67 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL F 146 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG F 95 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL F 146 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 97 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA F 148 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP F 99 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU F 150 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.454A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 71 through 74 Processing sheet with id= Q, first strand: chain 'G' and resid 86 through 89 Processing sheet with id= R, first strand: chain 'G' and resid 128 through 132 removed outlier: 5.817A pdb=" N ASP G 132 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL G 121 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 198 through 201 Processing sheet with id= T, first strand: chain 'H' and resid 45 through 47 Processing sheet with id= U, first strand: chain 'H' and resid 58 through 62 removed outlier: 3.911A pdb=" N SER H 59 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 106 through 109 removed outlier: 5.682A pdb=" N GLU H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE H 88 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.894A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 26 through 29 Processing sheet with id= Y, first strand: chain 'I' and resid 40 through 45 removed outlier: 5.777A pdb=" N SER I 21 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL I 55 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY I 23 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 131 through 134 removed outlier: 6.589A pdb=" N LEU I 143 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER I 77 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS I 86 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL I 75 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 127 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL I 155 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU I 129 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL I 153 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 2 through 10 Processing sheet with id= AB, first strand: chain 'K' and resid 87 through 90 removed outlier: 5.915A pdb=" N HIS K 119 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL K 90 " --> pdb=" O HIS K 119 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR K 121 " --> pdb=" O VAL K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'K' and resid 274 through 277 Processing sheet with id= AD, first strand: chain 'K' and resid 383 through 385 Processing sheet with id= AE, first strand: chain 'K' and resid 489 through 494 removed outlier: 3.964A pdb=" N LYS K 574 " --> pdb=" O GLU K 565 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 688 through 691 Processing sheet with id= AG, first strand: chain 'K' and resid 862 through 864 Processing sheet with id= AH, first strand: chain 'K' and resid 886 through 888 Processing sheet with id= AI, first strand: chain 'K' and resid 908 through 911 Processing sheet with id= AJ, first strand: chain 'K' and resid 396 through 399 removed outlier: 3.931A pdb=" N GLY K 421 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE K 399 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN K 419 " --> pdb=" O ILE K 399 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 99 through 103 removed outlier: 7.162A pdb=" N SER M 156 " --> pdb=" O HIS M 305 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE M 307 " --> pdb=" O SER M 156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU M 158 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR M 309 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER M 160 " --> pdb=" O THR M 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 161 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG M 184 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL M 249 " --> pdb=" O ARG M 184 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE M 186 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE M 251 " --> pdb=" O ILE M 186 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR M 188 " --> pdb=" O PHE M 251 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY M 210 " --> pdb=" O VAL M 226 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 452 through 455 removed outlier: 6.460A pdb=" N ALA M 478 " --> pdb=" O GLY M 453 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS M 455 " --> pdb=" O ALA M 478 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE M 480 " --> pdb=" O HIS M 455 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL M 389 " --> pdb=" O LEU M 479 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA M 481 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE M 391 " --> pdb=" O ALA M 481 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR M 495 " --> pdb=" O ILE M 390 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE M 392 " --> pdb=" O THR M 495 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU M 497 " --> pdb=" O PHE M 392 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE M 534 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE M 498 " --> pdb=" O ILE M 534 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE M 536 " --> pdb=" O PHE M 498 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS M 318 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL M 332 " --> pdb=" O HIS M 318 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE M 320 " --> pdb=" O LEU M 330 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU M 330 " --> pdb=" O ILE M 320 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 13.02 Time building geometry restraints manager: 14.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10430 1.34 - 1.46: 5378 1.46 - 1.58: 16070 1.58 - 1.69: 120 1.69 - 1.81: 291 Bond restraints: 32289 Sorted by residual: bond pdb=" O3A ANP M2001 " pdb=" PB ANP M2001 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 1.593 1.681 -0.088 1.50e-02 4.44e+03 3.41e+01 bond pdb=" P C O 17 " pdb=" OP1 C O 17 " ideal model delta sigma weight residual 1.485 1.568 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ANP M2001 " pdb=" PA ANP M2001 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.22e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.30: 851 105.30 - 112.48: 17002 112.48 - 119.66: 10396 119.66 - 126.85: 15165 126.85 - 134.03: 461 Bond angle restraints: 43875 Sorted by residual: angle pdb=" CA PRO K 648 " pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 112.00 99.55 12.45 1.40e+00 5.10e-01 7.90e+01 angle pdb=" O3' DT O 16 " pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 104.00 115.00 -11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" O1B ANP M2001 " pdb=" PB ANP M2001 " pdb=" O2B ANP M2001 " ideal model delta sigma weight residual 120.08 109.31 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C HIS M 278 " pdb=" N TYR M 279 " pdb=" CA TYR M 279 " ideal model delta sigma weight residual 122.09 116.39 5.70 1.86e+00 2.89e-01 9.38e+00 angle pdb=" N ALA K 600 " pdb=" CA ALA K 600 " pdb=" CB ALA K 600 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 ... (remaining 43870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 19472 33.55 - 67.10: 167 67.10 - 100.65: 15 100.65 - 134.20: 1 134.20 - 167.76: 2 Dihedral angle restraints: 19657 sinusoidal: 8432 harmonic: 11225 Sorted by residual: dihedral pdb=" CA MET K 455 " pdb=" C MET K 455 " pdb=" N PRO K 456 " pdb=" CA PRO K 456 " ideal model delta harmonic sigma weight residual 180.00 131.40 48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" O4' C O 49 " pdb=" C1' C O 49 " pdb=" N1 C O 49 " pdb=" C2 C O 49 " ideal model delta sinusoidal sigma weight residual -128.00 32.68 -160.68 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA ASP B 201 " pdb=" C ASP B 201 " pdb=" N ALA B 202 " pdb=" CA ALA B 202 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 19654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5007 0.119 - 0.238: 45 0.238 - 0.357: 1 0.357 - 0.476: 0 0.476 - 0.595: 1 Chirality restraints: 5054 Sorted by residual: chirality pdb=" P C O 17 " pdb=" OP1 C O 17 " pdb=" OP2 C O 17 " pdb=" O5' C O 17 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" C3' ANP M2001 " pdb=" C2' ANP M2001 " pdb=" C4' ANP M2001 " pdb=" O3' ANP M2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1' A O 58 " pdb=" O4' A O 58 " pdb=" C2' A O 58 " pdb=" N9 A O 58 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5051 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C O 42 " 0.040 2.00e-02 2.50e+03 2.04e-02 9.39e+00 pdb=" N1 C O 42 " -0.043 2.00e-02 2.50e+03 pdb=" C2 C O 42 " -0.010 2.00e-02 2.50e+03 pdb=" O2 C O 42 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C O 42 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C O 42 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C O 42 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C O 42 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C O 42 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 60 " 0.035 2.00e-02 2.50e+03 1.59e-02 6.92e+00 pdb=" N9 A O 60 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A O 60 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A O 60 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A O 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A O 60 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A O 60 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A O 60 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 41 " 0.034 2.00e-02 2.50e+03 1.48e-02 6.05e+00 pdb=" N9 A O 41 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A O 41 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A O 41 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A O 41 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A O 41 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A O 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 157 2.43 - 3.05: 22069 3.05 - 3.67: 44805 3.67 - 4.28: 67541 4.28 - 4.90: 113573 Nonbonded interactions: 248145 Sorted by model distance: nonbonded pdb=" O2' C O 42 " pdb=" O5' A O 43 " model vdw 1.816 2.440 nonbonded pdb=" OG SER B 7 " pdb=" OE1 GLN B 9 " model vdw 1.944 2.440 nonbonded pdb=" OG SER M 189 " pdb=" OG SER M 195 " model vdw 1.956 2.440 nonbonded pdb=" OD1 ASP C 111 " pdb=" ND2 ASN C 115 " model vdw 1.959 2.520 nonbonded pdb=" OE2 GLU M 267 " pdb=" OG SER M 561 " model vdw 1.979 2.440 ... (remaining 248140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 196 5.16 5 C 19695 2.51 5 N 5611 2.21 5 O 6074 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.030 Extract box with map and model: 14.320 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.280 Process input model: 95.570 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.008 0.142 32289 Z= 0.520 Angle : 0.680 12.446 43875 Z= 0.376 Chirality : 0.045 0.595 5054 Planarity : 0.004 0.051 5456 Dihedral : 10.123 167.755 12393 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -4.48 (0.11), residues: 3839 helix: -1.97 (0.12), residues: 1234 sheet: -2.38 (0.17), residues: 762 loop : -4.04 (0.10), residues: 1843 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 769 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 770 average time/residue: 0.4923 time to fit residues: 572.0109 Evaluate side-chains 382 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.0770 chunk 293 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 225 optimal weight: 0.0070 chunk 351 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 188 HIS B 33 GLN E 19 GLN E 114 ASN E 131 HIS F 15 GLN G 116 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN L 20 GLN L 92 ASN M 300 HIS ** M 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 981 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 32289 Z= 0.190 Angle : 0.621 12.246 43875 Z= 0.317 Chirality : 0.043 0.254 5054 Planarity : 0.004 0.084 5456 Dihedral : 9.161 170.905 4917 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.46 (0.13), residues: 3839 helix: 0.03 (0.14), residues: 1239 sheet: -1.70 (0.18), residues: 771 loop : -2.85 (0.13), residues: 1829 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 453 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 490 average time/residue: 0.4489 time to fit residues: 347.9348 Evaluate side-chains 378 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 346 time to evaluate : 3.989 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3127 time to fit residues: 23.5045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 292 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 352 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 313 optimal weight: 0.3980 chunk 349 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 282 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN H 64 ASN H 93 GLN H 101 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN K 919 GLN M 300 HIS M 317 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 32289 Z= 0.190 Angle : 0.566 8.782 43875 Z= 0.288 Chirality : 0.042 0.289 5054 Planarity : 0.004 0.078 5456 Dihedral : 9.030 174.515 4917 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.57 (0.13), residues: 3839 helix: 0.73 (0.15), residues: 1252 sheet: -1.16 (0.18), residues: 764 loop : -2.32 (0.13), residues: 1823 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 399 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 25 residues processed: 436 average time/residue: 0.4364 time to fit residues: 306.1837 Evaluate side-chains 355 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 330 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3103 time to fit residues: 19.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 168 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 120 GLN D 30 HIS F 249 GLN H 64 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN M 342 ASN M1006 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.153 32289 Z= 0.339 Angle : 0.654 18.419 43875 Z= 0.330 Chirality : 0.044 0.288 5054 Planarity : 0.005 0.118 5456 Dihedral : 9.151 176.134 4917 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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 (0.13), residues: 3839 helix: 0.76 (0.15), residues: 1248 sheet: -0.89 (0.18), residues: 745 loop : -2.07 (0.14), residues: 1846 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 367 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 39 residues processed: 419 average time/residue: 0.4347 time to fit residues: 294.2059 Evaluate side-chains 370 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 331 time to evaluate : 3.969 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3232 time to fit residues: 28.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 1.9990 chunk 212 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 319 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 335 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 32289 Z= 0.232 Angle : 0.577 8.743 43875 Z= 0.292 Chirality : 0.042 0.299 5054 Planarity : 0.004 0.082 5456 Dihedral : 9.024 174.919 4917 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.99 (0.13), residues: 3839 helix: 1.04 (0.15), residues: 1246 sheet: -0.71 (0.19), residues: 734 loop : -1.87 (0.14), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 363 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 386 average time/residue: 0.4479 time to fit residues: 277.8830 Evaluate side-chains 342 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 326 time to evaluate : 3.737 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3038 time to fit residues: 13.8632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.3980 chunk 336 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS H 64 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 32289 Z= 0.198 Angle : 0.558 12.055 43875 Z= 0.280 Chirality : 0.041 0.298 5054 Planarity : 0.004 0.094 5456 Dihedral : 8.945 174.461 4917 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.75 (0.14), residues: 3839 helix: 1.20 (0.15), residues: 1256 sheet: -0.52 (0.19), residues: 744 loop : -1.73 (0.14), residues: 1839 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 351 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 18 residues processed: 382 average time/residue: 0.4405 time to fit residues: 270.5597 Evaluate side-chains 337 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 319 time to evaluate : 4.117 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3338 time to fit residues: 16.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS G 88 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.118 32289 Z= 0.326 Angle : 0.624 9.817 43875 Z= 0.313 Chirality : 0.043 0.275 5054 Planarity : 0.004 0.103 5456 Dihedral : 9.015 176.221 4917 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.78 (0.13), residues: 3839 helix: 1.10 (0.15), residues: 1249 sheet: -0.47 (0.19), residues: 741 loop : -1.72 (0.14), residues: 1849 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 333 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 368 average time/residue: 0.4530 time to fit residues: 267.8848 Evaluate side-chains 336 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 314 time to evaluate : 4.068 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2999 time to fit residues: 17.6125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 293 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS H 64 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN K 760 ASN M 898 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.137 32289 Z= 0.291 Angle : 0.615 12.180 43875 Z= 0.309 Chirality : 0.042 0.273 5054 Planarity : 0.004 0.107 5456 Dihedral : 8.984 175.521 4917 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.71 (0.13), residues: 3839 helix: 1.09 (0.15), residues: 1257 sheet: -0.39 (0.19), residues: 744 loop : -1.66 (0.14), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 354 average time/residue: 0.4403 time to fit residues: 253.2298 Evaluate side-chains 328 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 312 time to evaluate : 3.707 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2946 time to fit residues: 13.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS E 275 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.189 32289 Z= 0.310 Angle : 0.627 13.510 43875 Z= 0.316 Chirality : 0.042 0.262 5054 Planarity : 0.004 0.110 5456 Dihedral : 8.965 175.791 4917 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.67 (0.13), residues: 3839 helix: 1.11 (0.15), residues: 1253 sheet: -0.31 (0.19), residues: 743 loop : -1.64 (0.14), residues: 1843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 323 time to evaluate : 4.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 337 average time/residue: 0.4436 time to fit residues: 241.1944 Evaluate side-chains 320 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 3.741 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2849 time to fit residues: 11.6430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 4.9990 chunk 367 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 0.0770 chunk 255 optimal weight: 0.8980 chunk 385 optimal weight: 9.9990 chunk 354 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN C 120 GLN D 30 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.444 32289 Z= 0.301 Angle : 0.607 20.848 43875 Z= 0.310 Chirality : 0.041 0.260 5054 Planarity : 0.004 0.117 5456 Dihedral : 8.918 174.875 4917 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.53 (0.14), residues: 3839 helix: 1.23 (0.15), residues: 1257 sheet: -0.21 (0.19), residues: 744 loop : -1.57 (0.14), residues: 1838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 330 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 336 average time/residue: 0.4614 time to fit residues: 248.7335 Evaluate side-chains 320 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 314 time to evaluate : 3.833 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3005 time to fit residues: 9.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 283 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 315 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS F 221 GLN H 64 ASN H 93 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 317 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086251 restraints weight = 62917.452| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.15 r_work: 0.3187 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3161 rms_B_bonded: 1.98 restraints_weight: 0.1250 r_work: 0.3147 rms_B_bonded: 2.08 restraints_weight: 0.0625 r_work: 0.3131 rms_B_bonded: 2.22 restraints_weight: 0.0312 r_work: 0.3114 rms_B_bonded: 2.40 restraints_weight: 0.0156 r_work: 0.3095 rms_B_bonded: 2.64 restraints_weight: 0.0078 r_work: 0.3074 rms_B_bonded: 2.92 restraints_weight: 0.0039 r_work: 0.3050 rms_B_bonded: 3.27 restraints_weight: 0.0020 r_work: 0.3023 rms_B_bonded: 3.68 restraints_weight: 0.0010 r_work: 0.2993 rms_B_bonded: 4.18 restraints_weight: 0.0005 r_work: 0.2959 rms_B_bonded: 4.77 restraints_weight: 0.0002 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.165 32289 Z= 0.251 Angle : 0.604 19.175 43875 Z= 0.307 Chirality : 0.041 0.251 5054 Planarity : 0.005 0.180 5456 Dihedral : 8.909 175.094 4917 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.50 (0.14), residues: 3839 helix: 1.24 (0.15), residues: 1252 sheet: -0.19 (0.19), residues: 744 loop : -1.55 (0.14), residues: 1843 =============================================================================== Job complete usr+sys time: 6699.40 seconds wall clock time: 122 minutes 32.06 seconds (7352.06 seconds total)