Starting phenix.real_space_refine on Wed Feb 21 19:19:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2024/6d6r_7809_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2024/6d6r_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_7809/02_2024/6d6r_7809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2024/6d6r_7809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2024/6d6r_7809_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6r_7809/02_2024/6d6r_7809_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5238/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: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 683} 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: {'DNA': 13, 'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 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: {' MG': 1, ' ZN': 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: 16.02, per 1000 atoms: 0.51 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: 12.78 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal 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: 13.17 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: 13.01 Time building geometry restraints manager: 13.59 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: 19538 33.55 - 67.10: 210 67.10 - 100.65: 32 100.65 - 134.20: 1 134.20 - 167.76: 2 Dihedral angle restraints: 19783 sinusoidal: 8558 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 19780 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 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: 2.810 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: 0.040 Extract box with map and model: 13.000 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 95.780 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 10.881 167.755 12519 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 405 HIS 0.011 0.002 HIS C 236 PHE 0.027 0.002 PHE C 154 TYR 0.039 0.002 TYR M 279 ARG 0.008 0.001 ARG K 285 *********************** 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 : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ARG cc_start: 0.7300 (mpt-90) cc_final: 0.6949 (mmt90) REVERT: C 9 GLU cc_start: 0.5666 (mp0) cc_final: 0.4826 (pt0) REVERT: C 34 THR cc_start: 0.8801 (m) cc_final: 0.8332 (p) REVERT: C 226 MET cc_start: 0.7587 (tpt) cc_final: 0.7377 (tpt) REVERT: D 68 LYS cc_start: 0.7050 (mtmp) cc_final: 0.6777 (mtpt) REVERT: E 233 LYS cc_start: 0.8184 (mptp) cc_final: 0.7883 (mttp) REVERT: F 50 LYS cc_start: 0.8704 (tttt) cc_final: 0.8451 (tttp) REVERT: G 162 LEU cc_start: 0.8217 (pt) cc_final: 0.8015 (pt) REVERT: H 82 ASP cc_start: 0.7349 (m-30) cc_final: 0.7121 (m-30) REVERT: H 271 ILE cc_start: 0.8078 (pp) cc_final: 0.7827 (pt) REVERT: K 166 ASP cc_start: 0.4839 (m-30) cc_final: 0.4566 (m-30) REVERT: K 238 GLN cc_start: 0.6873 (pt0) cc_final: 0.6586 (mm-40) REVERT: K 265 ILE cc_start: 0.6802 (mm) cc_final: 0.6345 (mm) REVERT: K 470 LEU cc_start: 0.8314 (mp) cc_final: 0.7914 (mp) REVERT: K 488 ASP cc_start: 0.7209 (m-30) cc_final: 0.6921 (m-30) REVERT: K 926 SER cc_start: 0.8475 (m) cc_final: 0.8265 (p) REVERT: L 63 SER cc_start: 0.8930 (t) cc_final: 0.7941 (p) REVERT: L 67 CYS cc_start: 0.7796 (t) cc_final: 0.7438 (m) REVERT: M 329 HIS cc_start: 0.8282 (m90) cc_final: 0.7922 (m90) REVERT: M 489 ILE cc_start: 0.7302 (pp) cc_final: 0.7085 (pp) outliers start: 1 outliers final: 0 residues processed: 770 average time/residue: 0.5099 time to fit residues: 587.9567 Evaluate side-chains 391 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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: 0.9990 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 351 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 101 ASN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32289 Z= 0.211 Angle : 0.623 9.920 43875 Z= 0.318 Chirality : 0.043 0.250 5054 Planarity : 0.004 0.056 5456 Dihedral : 10.985 169.881 5043 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.60 % Allowed : 8.26 % Favored : 90.14 % 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: -2.53 (0.13), residues: 3839 helix: -0.02 (0.14), residues: 1238 sheet: -1.71 (0.18), residues: 770 loop : -2.91 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 564 HIS 0.011 0.001 HIS M 981 PHE 0.026 0.002 PHE L 57 TYR 0.031 0.002 TYR M 279 ARG 0.007 0.000 ARG G 77 *********************** 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: 53 poor density : 454 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7404 (pp) REVERT: A 229 ARG cc_start: 0.7435 (mpt-90) cc_final: 0.7113 (mmt90) REVERT: A 240 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6441 (pp) REVERT: B 22 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7853 (ptt90) REVERT: C 9 GLU cc_start: 0.5639 (mp0) cc_final: 0.5035 (pt0) REVERT: C 34 THR cc_start: 0.8723 (m) cc_final: 0.8339 (p) REVERT: D 63 GLU cc_start: 0.7251 (tt0) cc_final: 0.7033 (tt0) REVERT: D 143 ASP cc_start: 0.7968 (t70) cc_final: 0.7750 (t0) REVERT: E 233 LYS cc_start: 0.8217 (mptp) cc_final: 0.7844 (mttp) REVERT: F 50 LYS cc_start: 0.8772 (tttt) cc_final: 0.8388 (tttp) REVERT: F 111 ARG cc_start: 0.7044 (ptp-110) cc_final: 0.6639 (mtp85) REVERT: G 164 TYR cc_start: 0.8745 (t80) cc_final: 0.8429 (t80) REVERT: G 173 ASP cc_start: 0.7423 (m-30) cc_final: 0.7196 (m-30) REVERT: H 105 ASP cc_start: 0.7195 (t0) cc_final: 0.6952 (t70) REVERT: H 128 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 129 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8294 (mm) REVERT: H 271 ILE cc_start: 0.8300 (pp) cc_final: 0.8056 (pt) REVERT: K 96 GLN cc_start: 0.7034 (tt0) cc_final: 0.6808 (tm-30) REVERT: K 238 GLN cc_start: 0.6614 (pt0) cc_final: 0.6394 (mm-40) REVERT: K 265 ILE cc_start: 0.7102 (mm) cc_final: 0.6487 (mm) REVERT: K 926 SER cc_start: 0.8423 (m) cc_final: 0.8139 (p) REVERT: L 63 SER cc_start: 0.8903 (t) cc_final: 0.8220 (p) REVERT: L 91 MET cc_start: 0.8513 (mmm) cc_final: 0.7797 (mtt) REVERT: M 426 ASN cc_start: 0.8041 (m110) cc_final: 0.7653 (m110) REVERT: M 527 ARG cc_start: 0.6538 (ttm-80) cc_final: 0.6318 (ttm-80) outliers start: 53 outliers final: 33 residues processed: 490 average time/residue: 0.4621 time to fit residues: 355.6290 Evaluate side-chains 397 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 360 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 968 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 292 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 352 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 313 optimal weight: 0.3980 chunk 349 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 119 GLN G 105 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 GLN M 300 HIS M 317 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 32289 Z= 0.163 Angle : 0.553 8.700 43875 Z= 0.282 Chirality : 0.041 0.291 5054 Planarity : 0.004 0.058 5456 Dihedral : 10.781 173.037 5043 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.05 % Allowed : 9.95 % Favored : 88.00 % 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: -1.55 (0.13), residues: 3839 helix: 0.75 (0.15), residues: 1252 sheet: -1.14 (0.18), residues: 764 loop : -2.31 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 564 HIS 0.007 0.001 HIS K 64 PHE 0.014 0.001 PHE M 563 TYR 0.019 0.001 TYR K 772 ARG 0.028 0.000 ARG K 396 *********************** 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 476 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 408 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7233 (pp) REVERT: B 22 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7874 (ptt90) REVERT: B 56 GLU cc_start: 0.7315 (tp30) cc_final: 0.6472 (tp30) REVERT: C 34 THR cc_start: 0.8742 (m) cc_final: 0.8340 (p) REVERT: E 233 LYS cc_start: 0.8288 (mptp) cc_final: 0.7971 (mttp) REVERT: F 50 LYS cc_start: 0.8842 (tttt) cc_final: 0.8484 (tttp) REVERT: F 111 ARG cc_start: 0.7038 (ptp-110) cc_final: 0.6626 (mtp85) REVERT: G 103 ASP cc_start: 0.7114 (p0) cc_final: 0.6851 (p0) REVERT: G 164 TYR cc_start: 0.8739 (t80) cc_final: 0.8431 (t80) REVERT: H 129 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8142 (mm) REVERT: K 265 ILE cc_start: 0.7331 (mm) cc_final: 0.6654 (mm) REVERT: K 583 ASN cc_start: 0.8046 (p0) cc_final: 0.7801 (p0) REVERT: M 317 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: M 319 TYR cc_start: 0.8795 (m-80) cc_final: 0.8369 (m-80) REVERT: M 511 TRP cc_start: 0.8255 (m-10) cc_final: 0.8050 (m-10) REVERT: M 872 MET cc_start: 0.7947 (tpp) cc_final: 0.7730 (ttt) REVERT: M 973 TRP cc_start: 0.8123 (t-100) cc_final: 0.7911 (t-100) REVERT: M 1042 LEU cc_start: 0.7493 (mt) cc_final: 0.7290 (mt) outliers start: 68 outliers final: 40 residues processed: 458 average time/residue: 0.4359 time to fit residues: 318.8492 Evaluate side-chains 391 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 347 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 843 ASN Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 589 PHE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 0.8980 chunk 264 optimal weight: 0.0770 chunk 182 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 168 optimal weight: 0.0770 chunk 236 optimal weight: 3.9990 chunk 353 optimal weight: 10.0000 chunk 374 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9298 ------------------------------------------------------------------------------- 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 173 GLN F 249 GLN H 93 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 660 ASN M1006 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 32289 Z= 0.249 Angle : 0.580 9.210 43875 Z= 0.294 Chirality : 0.042 0.292 5054 Planarity : 0.004 0.059 5456 Dihedral : 10.763 174.002 5043 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.95 % Allowed : 11.54 % Favored : 85.50 % 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: -1.16 (0.13), residues: 3839 helix: 0.97 (0.15), residues: 1247 sheet: -0.86 (0.18), residues: 761 loop : -2.02 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 511 HIS 0.006 0.001 HIS C 236 PHE 0.018 0.002 PHE D 31 TYR 0.015 0.001 TYR H 252 ARG 0.006 0.000 ARG I 123 *********************** 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 468 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 370 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8539 (m-80) cc_final: 0.8137 (m-80) REVERT: A 105 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 121 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7410 (pp) REVERT: A 229 ARG cc_start: 0.7722 (mpt-90) cc_final: 0.7155 (mmt90) REVERT: A 240 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6686 (pp) REVERT: C 34 THR cc_start: 0.8831 (m) cc_final: 0.8457 (p) REVERT: C 226 MET cc_start: 0.8234 (tpt) cc_final: 0.7882 (tpt) REVERT: E 33 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6916 (ptt90) REVERT: E 74 PRO cc_start: 0.7854 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8363 (mptp) cc_final: 0.8012 (mttp) REVERT: F 50 LYS cc_start: 0.8919 (tttt) cc_final: 0.8564 (tttp) REVERT: F 111 ARG cc_start: 0.7163 (ptp-110) cc_final: 0.6748 (mtp85) REVERT: G 103 ASP cc_start: 0.7241 (p0) cc_final: 0.6741 (p0) REVERT: G 250 LEU cc_start: 0.8154 (tp) cc_final: 0.7817 (mt) REVERT: I 120 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7885 (mmmt) REVERT: K 172 ILE cc_start: 0.6435 (mm) cc_final: 0.6160 (mm) REVERT: K 265 ILE cc_start: 0.7495 (mm) cc_final: 0.6874 (mm) REVERT: K 470 LEU cc_start: 0.8619 (mp) cc_final: 0.8242 (tt) REVERT: K 583 ASN cc_start: 0.8265 (p0) cc_final: 0.8061 (p0) REVERT: K 926 SER cc_start: 0.8473 (m) cc_final: 0.8118 (p) REVERT: M 454 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9122 (pp) REVERT: M 529 MET cc_start: 0.8227 (mtm) cc_final: 0.7907 (mtp) REVERT: M 888 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7764 (mm) outliers start: 98 outliers final: 61 residues processed: 441 average time/residue: 0.4317 time to fit residues: 304.7162 Evaluate side-chains 407 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 340 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 843 ASN Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 298 HIS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 278 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 319 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 335 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 249 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 32289 Z= 0.217 Angle : 0.551 8.695 43875 Z= 0.279 Chirality : 0.041 0.295 5054 Planarity : 0.004 0.056 5456 Dihedral : 10.711 173.887 5043 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.80 % Allowed : 12.87 % Favored : 84.33 % 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: -0.89 (0.14), residues: 3839 helix: 1.13 (0.15), residues: 1248 sheet: -0.65 (0.19), residues: 772 loop : -1.83 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 564 HIS 0.005 0.001 HIS D 30 PHE 0.017 0.001 PHE B 106 TYR 0.016 0.001 TYR K 531 ARG 0.009 0.000 ARG L 78 *********************** 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 455 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 362 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 121 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7325 (pp) REVERT: A 147 ASP cc_start: 0.6872 (t70) cc_final: 0.6600 (t0) REVERT: A 229 ARG cc_start: 0.7733 (mpt-90) cc_final: 0.7160 (mmt90) REVERT: A 240 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6685 (pp) REVERT: B 22 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (ptt90) REVERT: B 186 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8130 (pt) REVERT: C 28 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 226 MET cc_start: 0.8262 (tpt) cc_final: 0.7947 (tpt) REVERT: E 33 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6865 (ptt90) REVERT: E 74 PRO cc_start: 0.7871 (Cg_endo) cc_final: 0.7534 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8453 (mptp) cc_final: 0.8089 (mttp) REVERT: F 50 LYS cc_start: 0.8897 (tttt) cc_final: 0.8530 (tttp) REVERT: F 111 ARG cc_start: 0.7256 (ptp-110) cc_final: 0.6849 (mtp85) REVERT: G 103 ASP cc_start: 0.7357 (p0) cc_final: 0.7034 (p0) REVERT: G 158 GLN cc_start: 0.7643 (mm110) cc_final: 0.7088 (mm-40) REVERT: G 161 ASP cc_start: 0.7542 (m-30) cc_final: 0.7333 (m-30) REVERT: G 250 LEU cc_start: 0.8169 (tp) cc_final: 0.7873 (mt) REVERT: H 107 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9146 (m) REVERT: K 265 ILE cc_start: 0.7533 (mm) cc_final: 0.6934 (mm) REVERT: K 470 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8347 (tp) REVERT: K 583 ASN cc_start: 0.8303 (p0) cc_final: 0.8039 (p0) REVERT: M 386 PHE cc_start: 0.8460 (m-10) cc_final: 0.8005 (m-10) REVERT: M 404 LEU cc_start: 0.8446 (mp) cc_final: 0.8126 (tp) REVERT: M 454 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9150 (pp) outliers start: 93 outliers final: 65 residues processed: 427 average time/residue: 0.4395 time to fit residues: 299.7971 Evaluate side-chains 406 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 332 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 968 ASP Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.5980 chunk 336 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32289 Z= 0.290 Angle : 0.597 10.717 43875 Z= 0.300 Chirality : 0.042 0.270 5054 Planarity : 0.004 0.057 5456 Dihedral : 10.747 175.303 5043 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.50 % Allowed : 13.14 % Favored : 83.36 % 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: 1.14 (0.15), residues: 1247 sheet: -0.48 (0.19), residues: 735 loop : -1.73 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 564 HIS 0.006 0.001 HIS D 30 PHE 0.024 0.002 PHE B 106 TYR 0.015 0.001 TYR F 252 ARG 0.005 0.000 ARG F 42 *********************** 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 471 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 355 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 121 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7521 (pp) REVERT: A 147 ASP cc_start: 0.6879 (t70) cc_final: 0.6596 (t0) REVERT: A 229 ARG cc_start: 0.7748 (mpt-90) cc_final: 0.7171 (mmt90) REVERT: A 240 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6943 (pp) REVERT: A 247 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7941 (t) REVERT: B 22 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8210 (ptt90) REVERT: B 186 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8187 (pt) REVERT: C 28 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 226 MET cc_start: 0.8403 (tpt) cc_final: 0.8063 (tpt) REVERT: E 33 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6987 (ptt90) REVERT: E 74 PRO cc_start: 0.7933 (Cg_endo) cc_final: 0.7630 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8541 (mptp) cc_final: 0.7926 (mttp) REVERT: F 50 LYS cc_start: 0.8931 (tttt) cc_final: 0.8482 (tttp) REVERT: F 111 ARG cc_start: 0.7290 (ptp-110) cc_final: 0.6904 (mtp85) REVERT: G 103 ASP cc_start: 0.7679 (p0) cc_final: 0.7394 (p0) REVERT: G 129 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7571 (p90) REVERT: H 228 LEU cc_start: 0.8454 (tt) cc_final: 0.8239 (tp) REVERT: K 265 ILE cc_start: 0.7639 (mm) cc_final: 0.7096 (mm) REVERT: K 470 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8331 (tt) REVERT: K 667 MET cc_start: 0.7218 (mmm) cc_final: 0.6826 (mmm) REVERT: M 386 PHE cc_start: 0.8569 (m-10) cc_final: 0.8038 (m-10) REVERT: M 404 LEU cc_start: 0.8493 (mp) cc_final: 0.8147 (tp) REVERT: M 454 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9149 (pp) REVERT: M 487 MET cc_start: 0.6519 (tpp) cc_final: 0.6191 (tpp) REVERT: M 543 MET cc_start: 0.6206 (mmp) cc_final: 0.5798 (mmt) REVERT: M 595 TYR cc_start: 0.6676 (m-10) cc_final: 0.6127 (m-10) REVERT: M 848 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7313 (ttt) REVERT: M 921 MET cc_start: 0.6652 (mmm) cc_final: 0.6072 (mmm) outliers start: 116 outliers final: 80 residues processed: 435 average time/residue: 0.4301 time to fit residues: 301.9497 Evaluate side-chains 421 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 330 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 298 HIS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 511 TRP Chi-restraints excluded: chain M residue 512 ILE Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 566 THR Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 848 MET Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL 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: 0.6980 chunk 213 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 0.0000 chunk 209 optimal weight: 0.8980 chunk 373 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 172 optimal weight: 0.2980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 660 ASN K 760 ASN M 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32289 Z= 0.170 Angle : 0.539 10.852 43875 Z= 0.272 Chirality : 0.040 0.277 5054 Planarity : 0.003 0.056 5456 Dihedral : 10.647 173.406 5043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.04 % Allowed : 14.23 % Favored : 82.73 % 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: 1.33 (0.15), residues: 1249 sheet: -0.30 (0.19), residues: 736 loop : -1.60 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 264 HIS 0.006 0.001 HIS D 30 PHE 0.014 0.001 PHE B 106 TYR 0.015 0.001 TYR H 252 ARG 0.007 0.000 ARG K 623 *********************** 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 452 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 351 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 121 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7256 (pp) REVERT: A 187 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6600 (pp) REVERT: A 229 ARG cc_start: 0.7699 (mpt-90) cc_final: 0.7123 (mmt90) REVERT: A 240 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6678 (pp) REVERT: A 282 PHE cc_start: 0.7426 (m-80) cc_final: 0.7198 (m-80) REVERT: B 22 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8087 (ptt90) REVERT: B 186 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8123 (pt) REVERT: C 28 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 226 MET cc_start: 0.8273 (tpt) cc_final: 0.8040 (tpt) REVERT: E 33 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6763 (ptt90) REVERT: E 74 PRO cc_start: 0.7835 (Cg_endo) cc_final: 0.7508 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8556 (mptp) cc_final: 0.7957 (mttp) REVERT: F 50 LYS cc_start: 0.8818 (tttt) cc_final: 0.8443 (tttp) REVERT: F 111 ARG cc_start: 0.7258 (ptp-110) cc_final: 0.6842 (mtp85) REVERT: G 103 ASP cc_start: 0.7686 (p0) cc_final: 0.7277 (p0) REVERT: G 129 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7452 (p90) REVERT: G 250 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8251 (mp) REVERT: H 220 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.6991 (mm) REVERT: K 64 HIS cc_start: 0.7072 (t70) cc_final: 0.6846 (t70) REVERT: K 265 ILE cc_start: 0.7794 (mm) cc_final: 0.7117 (mm) REVERT: K 470 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8320 (tt) REVERT: K 583 ASN cc_start: 0.8305 (p0) cc_final: 0.8003 (p0) REVERT: K 667 MET cc_start: 0.7155 (mmm) cc_final: 0.6804 (mmm) REVERT: K 817 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6862 (tt) REVERT: L 91 MET cc_start: 0.8549 (mmm) cc_final: 0.8106 (mtt) REVERT: M 227 MET cc_start: 0.7108 (ptt) cc_final: 0.6551 (ptt) REVERT: M 404 LEU cc_start: 0.8470 (mp) cc_final: 0.8116 (tp) REVERT: M 454 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9092 (pp) REVERT: M 487 MET cc_start: 0.6386 (tpp) cc_final: 0.6126 (tpp) REVERT: M 543 MET cc_start: 0.6078 (mmp) cc_final: 0.5283 (mmt) REVERT: M 973 TRP cc_start: 0.8223 (t-100) cc_final: 0.7964 (t-100) outliers start: 101 outliers final: 66 residues processed: 423 average time/residue: 0.4286 time to fit residues: 294.3820 Evaluate side-chains 403 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 324 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 377 ASP Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 566 MET Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 511 TRP Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1017 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 222 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 286 GLN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 898 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32289 Z= 0.210 Angle : 0.553 10.701 43875 Z= 0.278 Chirality : 0.040 0.249 5054 Planarity : 0.003 0.058 5456 Dihedral : 10.645 174.406 5043 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.47 % Allowed : 13.80 % Favored : 82.73 % 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: -0.48 (0.14), residues: 3839 helix: 1.30 (0.15), residues: 1259 sheet: -0.17 (0.19), residues: 728 loop : -1.57 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 973 HIS 0.004 0.001 HIS C 236 PHE 0.038 0.001 PHE K 666 TYR 0.015 0.001 TYR K 531 ARG 0.007 0.000 ARG K 623 *********************** 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 451 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 336 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 121 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 187 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6631 (pp) REVERT: A 229 ARG cc_start: 0.7699 (mpt-90) cc_final: 0.7128 (mmt90) REVERT: A 240 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6722 (pp) REVERT: A 282 PHE cc_start: 0.7365 (m-80) cc_final: 0.7134 (m-80) REVERT: B 186 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8168 (pt) REVERT: C 28 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 213 GLU cc_start: 0.7073 (pm20) cc_final: 0.6859 (pt0) REVERT: C 226 MET cc_start: 0.8329 (tpt) cc_final: 0.8102 (tpt) REVERT: E 33 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6865 (ptt90) REVERT: E 74 PRO cc_start: 0.7833 (Cg_endo) cc_final: 0.7506 (Cg_exo) REVERT: E 217 GLN cc_start: 0.8156 (mp10) cc_final: 0.7776 (mp10) REVERT: E 233 LYS cc_start: 0.8552 (mptp) cc_final: 0.8229 (mttp) REVERT: F 50 LYS cc_start: 0.8849 (tttt) cc_final: 0.8427 (tttp) REVERT: F 111 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.6910 (mtp85) REVERT: G 103 ASP cc_start: 0.7757 (p0) cc_final: 0.7356 (p0) REVERT: G 129 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7484 (p90) REVERT: G 250 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8032 (mp) REVERT: H 131 MET cc_start: 0.8068 (ttm) cc_final: 0.7795 (ttm) REVERT: H 220 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7109 (mm) REVERT: H 228 LEU cc_start: 0.8403 (tt) cc_final: 0.8184 (tp) REVERT: I 120 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7584 (mmmt) REVERT: K 265 ILE cc_start: 0.7792 (mm) cc_final: 0.7175 (mm) REVERT: K 470 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8340 (tt) REVERT: K 667 MET cc_start: 0.7253 (mmm) cc_final: 0.7000 (mmm) REVERT: K 817 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6899 (tt) REVERT: L 91 MET cc_start: 0.8501 (mmm) cc_final: 0.8094 (mtt) REVERT: M 227 MET cc_start: 0.7760 (ptt) cc_final: 0.7398 (ptt) REVERT: M 404 LEU cc_start: 0.8427 (mp) cc_final: 0.8061 (tp) REVERT: M 454 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9095 (pp) REVERT: M 595 TYR cc_start: 0.6339 (m-10) cc_final: 0.6048 (m-10) outliers start: 115 outliers final: 79 residues processed: 415 average time/residue: 0.4199 time to fit residues: 283.7123 Evaluate side-chains 421 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 330 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 431 GLU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 380 MET Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 272 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 314 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 F 221 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 32289 Z= 0.249 Angle : 0.580 11.155 43875 Z= 0.289 Chirality : 0.041 0.236 5054 Planarity : 0.004 0.053 5456 Dihedral : 10.662 174.930 5043 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.29 % Allowed : 14.38 % Favored : 82.34 % 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: -0.46 (0.14), residues: 3839 helix: 1.25 (0.15), residues: 1268 sheet: -0.12 (0.19), residues: 735 loop : -1.54 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 973 HIS 0.006 0.001 HIS D 30 PHE 0.030 0.002 PHE K 666 TYR 0.015 0.001 TYR I 119 ARG 0.006 0.000 ARG K 623 *********************** 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 458 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 349 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 121 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7479 (pp) REVERT: A 187 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6763 (pp) REVERT: A 229 ARG cc_start: 0.7670 (mpt-90) cc_final: 0.7121 (mmt90) REVERT: A 240 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6830 (pp) REVERT: B 22 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8435 (ptt90) REVERT: B 186 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (pt) REVERT: C 226 MET cc_start: 0.8393 (tpt) cc_final: 0.8131 (tpt) REVERT: D 205 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6807 (mt-10) REVERT: E 33 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6972 (ptt90) REVERT: E 217 GLN cc_start: 0.8209 (mp10) cc_final: 0.7917 (mp10) REVERT: E 233 LYS cc_start: 0.8581 (mptp) cc_final: 0.8234 (mttp) REVERT: F 50 LYS cc_start: 0.8899 (tttt) cc_final: 0.8465 (tttp) REVERT: F 111 ARG cc_start: 0.7320 (ptp-110) cc_final: 0.6928 (mtp85) REVERT: G 103 ASP cc_start: 0.7887 (p0) cc_final: 0.7503 (p0) REVERT: G 129 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7524 (p90) REVERT: H 220 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7092 (mm) REVERT: H 228 LEU cc_start: 0.8448 (tt) cc_final: 0.8225 (tp) REVERT: K 64 HIS cc_start: 0.7300 (t70) cc_final: 0.6920 (t70) REVERT: K 265 ILE cc_start: 0.7789 (mm) cc_final: 0.7187 (mm) REVERT: K 470 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8371 (tt) REVERT: K 817 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6969 (tt) REVERT: L 91 MET cc_start: 0.8496 (mmm) cc_final: 0.8126 (mtt) REVERT: M 404 LEU cc_start: 0.8394 (mp) cc_final: 0.8017 (tp) REVERT: M 454 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9094 (pp) REVERT: M 487 MET cc_start: 0.6530 (tpp) cc_final: 0.6074 (tpp) outliers start: 109 outliers final: 87 residues processed: 422 average time/residue: 0.4183 time to fit residues: 286.8603 Evaluate side-chains 431 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 332 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 377 ASP Chi-restraints excluded: chain K residue 431 GLU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 380 MET Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 512 ILE Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 566 THR Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 7.9990 chunk 367 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 385 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN F 221 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32289 Z= 0.311 Angle : 0.618 11.204 43875 Z= 0.309 Chirality : 0.042 0.223 5054 Planarity : 0.004 0.054 5456 Dihedral : 10.725 175.602 5043 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.10 % Allowed : 14.71 % Favored : 82.19 % 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: -0.54 (0.14), residues: 3839 helix: 1.15 (0.15), residues: 1265 sheet: -0.13 (0.19), residues: 734 loop : -1.56 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 973 HIS 0.010 0.001 HIS K 64 PHE 0.029 0.002 PHE K 666 TYR 0.019 0.002 TYR M 595 ARG 0.010 0.000 ARG M1032 ********************** 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 428 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 325 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 121 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7764 (pp) REVERT: A 187 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 229 ARG cc_start: 0.7700 (mpt-90) cc_final: 0.7161 (mmt90) REVERT: A 240 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6734 (pp) REVERT: B 186 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8249 (pt) REVERT: C 226 MET cc_start: 0.8443 (tpt) cc_final: 0.8152 (tpt) REVERT: E 33 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7080 (ptt90) REVERT: E 217 GLN cc_start: 0.8253 (mp10) cc_final: 0.7946 (mp10) REVERT: E 233 LYS cc_start: 0.8611 (mptp) cc_final: 0.8326 (mttp) REVERT: F 50 LYS cc_start: 0.8945 (tttt) cc_final: 0.8532 (tttp) REVERT: F 111 ARG cc_start: 0.7360 (ptp-110) cc_final: 0.6967 (mtp85) REVERT: G 103 ASP cc_start: 0.8003 (p0) cc_final: 0.7652 (p0) REVERT: G 129 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7581 (p90) REVERT: H 220 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7025 (mm) REVERT: H 228 LEU cc_start: 0.8557 (tt) cc_final: 0.8339 (tp) REVERT: I 30 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7119 (p-80) REVERT: I 120 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7741 (mmmt) REVERT: K 265 ILE cc_start: 0.7836 (mm) cc_final: 0.7279 (mm) REVERT: K 817 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7041 (tt) REVERT: L 91 MET cc_start: 0.8523 (mmm) cc_final: 0.8138 (mtt) REVERT: M 454 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9109 (pp) REVERT: M 487 MET cc_start: 0.6804 (tpp) cc_final: 0.6448 (tpp) REVERT: M 872 MET cc_start: 0.8268 (tpp) cc_final: 0.7770 (ttm) outliers start: 103 outliers final: 79 residues processed: 394 average time/residue: 0.4313 time to fit residues: 275.4683 Evaluate side-chains 408 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 318 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 377 ASP Chi-restraints excluded: chain K residue 431 GLU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 761 ASP Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 889 ASP Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 512 ILE Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 566 THR Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 3.9990 chunk 327 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 307 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086093 restraints weight = 62883.957| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.15 r_work: 0.3082 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 32289 Z= 0.221 Angle : 0.579 11.099 43875 Z= 0.289 Chirality : 0.041 0.224 5054 Planarity : 0.004 0.054 5456 Dihedral : 10.680 174.466 5043 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.65 % Allowed : 15.22 % Favored : 82.13 % 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: -0.43 (0.14), residues: 3839 helix: 1.25 (0.15), residues: 1267 sheet: -0.04 (0.19), residues: 726 loop : -1.52 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 973 HIS 0.005 0.001 HIS A 188 PHE 0.023 0.001 PHE K 666 TYR 0.019 0.001 TYR M 595 ARG 0.006 0.000 ARG M1032 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7779.92 seconds wall clock time: 141 minutes 6.47 seconds (8466.47 seconds total)