Starting phenix.real_space_refine on Mon Feb 19 23:57:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxy_35082/02_2024/8hxy_35082_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 340 5.49 5 S 84 5.16 5 C 15578 2.51 5 N 4681 2.21 5 O 5575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 812": "OE1" <-> "OE2" Residue "K GLU 878": "OE1" <-> "OE2" Residue "K GLU 1008": "OE1" <-> "OE2" Residue "K GLU 1160": "OE1" <-> "OE2" Residue "K GLU 1166": "OE1" <-> "OE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L GLU 260": "OE1" <-> "OE2" Residue "L GLU 289": "OE1" <-> "OE2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "M GLU 262": "OE1" <-> "OE2" Residue "M GLU 280": "OE1" <-> "OE2" Residue "M GLU 302": "OE1" <-> "OE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N GLU 260": "OE1" <-> "OE2" Residue "N GLU 359": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26263 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3466 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "J" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3504 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2398 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2769 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 319} Chain breaks: 3 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 272 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 66.840 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 64.280 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 63.351 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 74.553 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 74.084 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 71.437 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 74.678 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 42.378 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 41.569 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 41.271 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 44.417 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 41.810 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 40.876 1.00 59.47 S Time building chain proxies: 13.66, per 1000 atoms: 0.52 Number of scatterers: 26263 At special positions: 0 Unit cell: (139.65, 158.55, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 84 16.00 P 340 15.00 O 5575 8.00 N 4681 7.00 C 15578 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: 12.25 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" ND1 HIS N 283 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 266 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 263 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 286 " pdb=" ZN N 702 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 303 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 306 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 278 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 275 " pdb=" ZN N 703 " pdb="ZN ZN N 703 " - pdb=" ND1 HIS N 448 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 417 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 451 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 420 " pdb=" ZN N 704 " pdb="ZN ZN N 704 " - pdb=" NE2 HIS N 469 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 443 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 466 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 440 " Number of angles added : 15 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 9 sheets defined 49.9% alpha, 4.4% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 12.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 88 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.523A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.524A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.534A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.518A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER D 109 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 removed outlier: 4.204A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.512A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.027A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.644A pdb=" N LEU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.635A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.826A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER H 109 " --> pdb=" O HIS H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 676 removed outlier: 5.208A pdb=" N PHE K 669 " --> pdb=" O GLU K 665 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU K 670 " --> pdb=" O VAL K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 679 through 693 Processing helix chain 'K' and resid 699 through 709 Processing helix chain 'K' and resid 714 through 724 Processing helix chain 'K' and resid 760 through 763 No H-bonds generated for 'chain 'K' and resid 760 through 763' Processing helix chain 'K' and resid 772 through 777 Processing helix chain 'K' and resid 786 through 789 No H-bonds generated for 'chain 'K' and resid 786 through 789' Processing helix chain 'K' and resid 802 through 839 Processing helix chain 'K' and resid 853 through 856 removed outlier: 4.311A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 853 through 856' Processing helix chain 'K' and resid 862 through 870 Processing helix chain 'K' and resid 873 through 885 removed outlier: 4.344A pdb=" N PHE K 877 " --> pdb=" O LYS K 873 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 887 through 927 Proline residue: K 892 - end of helix removed outlier: 3.759A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) Processing helix chain 'K' and resid 935 through 942 Processing helix chain 'K' and resid 945 through 963 removed outlier: 3.637A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) Processing helix chain 'K' and resid 983 through 998 Processing helix chain 'K' and resid 1004 through 1021 Processing helix chain 'K' and resid 1026 through 1032 Processing helix chain 'K' and resid 1142 through 1163 removed outlier: 3.534A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) Processing helix chain 'K' and resid 1165 through 1173 Processing helix chain 'K' and resid 1179 through 1183 Processing helix chain 'K' and resid 1190 through 1193 No H-bonds generated for 'chain 'K' and resid 1190 through 1193' Processing helix chain 'K' and resid 1203 through 1216 Processing helix chain 'K' and resid 1221 through 1232 Processing helix chain 'K' and resid 1237 through 1239 No H-bonds generated for 'chain 'K' and resid 1237 through 1239' Processing helix chain 'K' and resid 1242 through 1257 Processing helix chain 'K' and resid 1263 through 1274 Processing helix chain 'K' and resid 1280 through 1293 removed outlier: 3.606A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 42 through 54 removed outlier: 3.994A pdb=" N MET L 47 " --> pdb=" O ARG L 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER L 50 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET L 53 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN L 54 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 80 through 88 Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 99 through 103 Processing helix chain 'L' and resid 116 through 135 Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'L' and resid 191 through 196 Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 244 through 261 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 288 through 301 removed outlier: 4.115A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE L 301 " --> pdb=" O TYR L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 330 removed outlier: 3.623A pdb=" N ASN L 330 " --> pdb=" O THR L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 346 No H-bonds generated for 'chain 'L' and resid 344 through 346' Processing helix chain 'L' and resid 366 through 382 removed outlier: 3.522A pdb=" N GLU L 381 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN L 382 " --> pdb=" O ALA L 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 102 through 130 Processing helix chain 'M' and resid 226 through 240 Processing helix chain 'M' and resid 255 through 265 removed outlier: 3.645A pdb=" N GLU M 262 " --> pdb=" O LEU M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 296 removed outlier: 4.770A pdb=" N GLY M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 315 Processing helix chain 'M' and resid 328 through 343 Proline residue: M 339 - end of helix Processing helix chain 'M' and resid 349 through 368 removed outlier: 3.988A pdb=" N MET M 368 " --> pdb=" O VAL M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 373 No H-bonds generated for 'chain 'M' and resid 370 through 373' Processing helix chain 'M' and resid 392 through 400 Processing helix chain 'N' and resid 121 through 127 removed outlier: 4.696A pdb=" N GLU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 175 No H-bonds generated for 'chain 'N' and resid 172 through 175' Processing helix chain 'N' and resid 304 through 314 Processing helix chain 'N' and resid 319 through 329 Processing helix chain 'N' and resid 337 through 342 Processing helix chain 'N' and resid 355 through 358 No H-bonds generated for 'chain 'N' and resid 355 through 358' Processing helix chain 'N' and resid 383 through 386 No H-bonds generated for 'chain 'N' and resid 383 through 386' Processing helix chain 'N' and resid 431 through 433 No H-bonds generated for 'chain 'N' and resid 431 through 433' Processing helix chain 'P' and resid 544 through 562 Processing sheet with id= A, first strand: chain 'K' and resid 975 through 978 removed outlier: 3.703A pdb=" N HIS K1311 " --> pdb=" O ASP K1306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K1306 " --> pdb=" O HIS K1311 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 62 through 64 removed outlier: 6.464A pdb=" N VAL L 141 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE L 24 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL L 143 " --> pdb=" O PHE L 24 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET L 305 " --> pdb=" O ALA L 142 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN L 144 " --> pdb=" O MET L 305 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL L 307 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 97 through 99 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'M' and resid 244 through 246 Processing sheet with id= F, first strand: chain 'N' and resid 272 through 274 Processing sheet with id= G, first strand: chain 'N' and resid 437 through 439 Processing sheet with id= H, first strand: chain 'N' and resid 473 through 477 Processing sheet with id= I, first strand: chain 'N' and resid 85 through 87 removed outlier: 3.642A pdb=" N GLU N 86 " --> pdb=" O LYS N 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS N 95 " --> pdb=" O GLU N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 826 hydrogen bonds defined for protein. 2346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 15.84 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4385 1.32 - 1.45: 8652 1.45 - 1.57: 13637 1.57 - 1.69: 679 1.69 - 1.81: 133 Bond restraints: 27486 Sorted by residual: bond pdb=" CA ARG L 44 " pdb=" C ARG L 44 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.37e-02 5.33e+03 2.83e+01 bond pdb=" CA ARG D 96 " pdb=" C ARG D 96 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.27e-02 6.20e+03 1.93e+01 bond pdb=" CA ASP N 261 " pdb=" C ASP N 261 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 27481 not shown) Histogram of bond angle deviations from ideal: 96.06 - 104.08: 1309 104.08 - 112.10: 14429 112.10 - 120.12: 11865 120.12 - 128.14: 10401 128.14 - 136.16: 551 Bond angle restraints: 38555 Sorted by residual: angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.12 104.02 8.10 8.40e-01 1.42e+00 9.30e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" C GLU A 133 " ideal model delta sigma weight residual 113.97 101.71 12.26 1.28e+00 6.10e-01 9.18e+01 angle pdb=" N HIS F 75 " pdb=" CA HIS F 75 " pdb=" C HIS F 75 " ideal model delta sigma weight residual 113.97 104.30 9.67 1.28e+00 6.10e-01 5.71e+01 angle pdb=" N GLY B 48 " pdb=" CA GLY B 48 " pdb=" C GLY B 48 " ideal model delta sigma weight residual 112.51 100.95 11.56 1.53e+00 4.27e-01 5.71e+01 angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.06 14.74 2.13e+00 2.20e-01 4.79e+01 ... (remaining 38550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 13846 35.95 - 71.89: 1821 71.89 - 107.84: 21 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 15693 sinusoidal: 8723 harmonic: 6970 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL K 923 " pdb=" C VAL K 923 " pdb=" N PHE K 924 " pdb=" CA PHE K 924 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 15690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3449 0.055 - 0.111: 689 0.111 - 0.166: 102 0.166 - 0.221: 17 0.221 - 0.277: 5 Chirality restraints: 4262 Sorted by residual: chirality pdb=" CB VAL L 363 " pdb=" CA VAL L 363 " pdb=" CG1 VAL L 363 " pdb=" CG2 VAL L 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4259 not shown) Planarity restraints: 3721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " 0.102 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO N 508 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C VAL A 101 " 0.090 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 72 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ARG A 72 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A 72 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.030 2.00e-02 2.50e+03 ... (remaining 3718 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 731 2.65 - 3.21: 23311 3.21 - 3.78: 48224 3.78 - 4.34: 63606 4.34 - 4.90: 93515 Nonbonded interactions: 229387 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 2.208 2.230 nonbonded pdb=" O ASN K 663 " pdb=" OG1 THR K 667 " model vdw 2.209 2.440 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.220 2.520 nonbonded pdb=" O ARG K1308 " pdb=" OG1 THR K1309 " model vdw 2.260 2.440 ... (remaining 229382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 34 or resid 37 through 134)) selection = (chain 'E' and (resid 12 through 13 or resid 18 or resid 38 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = (chain 'H' and resid 29 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.720 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: 0.050 Extract box with map and model: 4.820 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 87.920 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 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 : 0.007 0.079 27486 Z= 0.429 Angle : 0.941 18.278 38555 Z= 0.598 Chirality : 0.047 0.277 4262 Planarity : 0.007 0.149 3721 Dihedral : 23.635 179.735 11191 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.10 % Allowed : 15.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2335 helix: -1.21 (0.13), residues: 1222 sheet: -0.37 (0.47), residues: 122 loop : -1.16 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 PHE 0.039 0.002 PHE N 311 TYR 0.033 0.002 TYR A 99 ARG 0.012 0.001 ARG N 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 579 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7865 (t-90) cc_final: 0.7649 (t-90) REVERT: A 54 TYR cc_start: 0.5476 (m-10) cc_final: 0.5262 (m-10) REVERT: A 90 MET cc_start: 0.6059 (tpp) cc_final: 0.5647 (tpp) REVERT: B 31 LYS cc_start: 0.5974 (tttt) cc_final: 0.5748 (tttt) REVERT: B 79 LYS cc_start: 0.5816 (mmmm) cc_final: 0.5556 (mmtm) REVERT: B 96 THR cc_start: 0.6026 (p) cc_final: 0.5805 (p) REVERT: C 41 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7108 (mp0) REVERT: C 73 ASN cc_start: 0.6950 (t0) cc_final: 0.6593 (t0) REVERT: D 65 ASP cc_start: 0.7606 (t0) cc_final: 0.6972 (t0) REVERT: D 68 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6575 (tm-30) REVERT: D 79 HIS cc_start: 0.6219 (t-90) cc_final: 0.5864 (m170) REVERT: D 81 ASN cc_start: 0.7171 (m110) cc_final: 0.6655 (m110) REVERT: D 82 LYS cc_start: 0.7468 (tppt) cc_final: 0.7189 (mtmt) REVERT: E 90 MET cc_start: 0.6376 (mmm) cc_final: 0.6171 (mmp) REVERT: F 77 LYS cc_start: 0.7419 (mttt) cc_final: 0.7003 (mmtp) REVERT: F 78 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6737 (mtm-85) REVERT: F 79 LYS cc_start: 0.6333 (mttp) cc_final: 0.5989 (mtpp) REVERT: G 36 LYS cc_start: 0.7647 (mttt) cc_final: 0.7249 (mttp) REVERT: G 38 ASN cc_start: 0.6832 (m-40) cc_final: 0.6459 (m-40) REVERT: G 74 LYS cc_start: 0.6982 (ptmm) cc_final: 0.6726 (tptt) REVERT: G 104 GLN cc_start: 0.6964 (mt0) cc_final: 0.6283 (mm110) REVERT: H 83 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6471 (mmp80) REVERT: H 84 SER cc_start: 0.6461 (m) cc_final: 0.6220 (t) REVERT: H 96 ARG cc_start: 0.6857 (ttp80) cc_final: 0.6447 (ttp-110) REVERT: K 714 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7764 (mtmm) REVERT: K 764 PHE cc_start: 0.7104 (m-10) cc_final: 0.6761 (m-10) REVERT: K 812 GLU cc_start: 0.7776 (tp30) cc_final: 0.7399 (tp30) REVERT: K 828 ILE cc_start: 0.8109 (mt) cc_final: 0.7883 (mt) REVERT: K 958 ASP cc_start: 0.8312 (m-30) cc_final: 0.8001 (m-30) REVERT: K 1205 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7576 (mttt) REVERT: K 1227 SER cc_start: 0.8798 (t) cc_final: 0.8474 (p) REVERT: L 53 MET cc_start: 0.8718 (mmp) cc_final: 0.8122 (mmm) REVERT: L 100 GLU cc_start: 0.7964 (mp0) cc_final: 0.7629 (mt-10) REVERT: L 105 ASN cc_start: 0.7861 (t0) cc_final: 0.7358 (t0) REVERT: L 248 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7399 (ttt-90) REVERT: L 288 MET cc_start: 0.8275 (ttp) cc_final: 0.8026 (ttp) REVERT: M 296 MET cc_start: 0.7996 (ppp) cc_final: 0.7752 (ptp) REVERT: N 96 LEU cc_start: 0.5446 (pt) cc_final: 0.5190 (pt) REVERT: N 107 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7763 (ttpt) REVERT: N 117 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7339 (mmtt) REVERT: N 187 TRP cc_start: 0.6315 (m100) cc_final: 0.6082 (m100) REVERT: N 261 ASP cc_start: 0.8197 (m-30) cc_final: 0.7979 (m-30) REVERT: N 291 ILE cc_start: 0.7919 (mm) cc_final: 0.7581 (mt) REVERT: N 375 GLU cc_start: 0.7939 (pt0) cc_final: 0.7690 (pm20) REVERT: N 521 GLN cc_start: 0.7850 (tt0) cc_final: 0.7649 (tt0) outliers start: 2 outliers final: 1 residues processed: 579 average time/residue: 0.4668 time to fit residues: 397.7396 Evaluate side-chains 376 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 260 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 208 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 76 GLN C 68 ASN C 73 ASN C 112 GLN D 81 ASN D 92 GLN E 19 GLN E 39 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 73 ASN K 961 ASN K1311 HIS L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN M 389 ASN N 130 ASN N 430 HIS P 541 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27486 Z= 0.236 Angle : 0.567 7.930 38555 Z= 0.322 Chirality : 0.038 0.164 4262 Planarity : 0.005 0.086 3721 Dihedral : 26.888 176.343 6335 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.09 % Allowed : 17.98 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2335 helix: 0.28 (0.14), residues: 1253 sheet: -0.24 (0.48), residues: 121 loop : -0.76 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.005 0.001 HIS K 930 PHE 0.018 0.002 PHE M 17 TYR 0.030 0.002 TYR H 80 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 384 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7848 (t70) cc_final: 0.7372 (t-90) REVERT: A 74 ILE cc_start: 0.7848 (tp) cc_final: 0.7396 (tp) REVERT: A 79 LYS cc_start: 0.6857 (tttt) cc_final: 0.6655 (tttt) REVERT: A 129 ARG cc_start: 0.7050 (tpt90) cc_final: 0.6467 (tpt90) REVERT: B 77 LYS cc_start: 0.8232 (mttt) cc_final: 0.8026 (mttt) REVERT: B 93 GLN cc_start: 0.5088 (mm-40) cc_final: 0.4591 (mp10) REVERT: C 20 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7322 (ttm-80) REVERT: C 41 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 73 ASN cc_start: 0.6995 (t0) cc_final: 0.6529 (t0) REVERT: C 92 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 99 ARG cc_start: 0.6514 (ptm160) cc_final: 0.6306 (mtp85) REVERT: D 56 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6510 (tpp) REVERT: D 65 ASP cc_start: 0.7407 (t0) cc_final: 0.6906 (t0) REVERT: D 68 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6359 (mt-10) REVERT: D 73 GLU cc_start: 0.7582 (tp30) cc_final: 0.7326 (tp30) REVERT: D 79 HIS cc_start: 0.6710 (t-90) cc_final: 0.6373 (m170) REVERT: D 81 ASN cc_start: 0.7921 (m-40) cc_final: 0.7471 (m110) REVERT: D 82 LYS cc_start: 0.8048 (tppt) cc_final: 0.7661 (mtmt) REVERT: E 90 MET cc_start: 0.5887 (mmm) cc_final: 0.5676 (mmp) REVERT: F 44 LYS cc_start: 0.8342 (tttt) cc_final: 0.8141 (tttt) REVERT: F 74 GLU cc_start: 0.6220 (tt0) cc_final: 0.5877 (tm-30) REVERT: F 77 LYS cc_start: 0.8023 (mttt) cc_final: 0.7532 (mmtp) REVERT: F 79 LYS cc_start: 0.6726 (mttp) cc_final: 0.6251 (mmtm) REVERT: G 104 GLN cc_start: 0.7112 (mt0) cc_final: 0.6329 (mm110) REVERT: H 81 ASN cc_start: 0.7805 (m110) cc_final: 0.7413 (m110) REVERT: H 83 ARG cc_start: 0.6639 (mmt90) cc_final: 0.6398 (mmp80) REVERT: H 84 SER cc_start: 0.6066 (m) cc_final: 0.5742 (t) REVERT: K 764 PHE cc_start: 0.7410 (m-10) cc_final: 0.6960 (m-10) REVERT: K 812 GLU cc_start: 0.7830 (tp30) cc_final: 0.7503 (tp30) REVERT: K 957 VAL cc_start: 0.8858 (t) cc_final: 0.8569 (t) REVERT: K 958 ASP cc_start: 0.8277 (m-30) cc_final: 0.8038 (m-30) REVERT: K 1205 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7528 (mttt) REVERT: K 1227 SER cc_start: 0.8806 (t) cc_final: 0.8490 (p) REVERT: K 1287 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7680 (ttp80) REVERT: L 53 MET cc_start: 0.8824 (mmp) cc_final: 0.8244 (mmm) REVERT: L 61 MET cc_start: 0.8306 (ptp) cc_final: 0.8026 (ptp) REVERT: L 88 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7507 (mtp-110) REVERT: L 105 ASN cc_start: 0.7918 (t0) cc_final: 0.7389 (t0) REVERT: L 248 ARG cc_start: 0.7648 (ttt180) cc_final: 0.7336 (ttt-90) REVERT: L 288 MET cc_start: 0.8326 (ttp) cc_final: 0.8067 (ttp) REVERT: M 242 ASP cc_start: 0.8534 (m-30) cc_final: 0.8330 (m-30) REVERT: M 296 MET cc_start: 0.8067 (ppp) cc_final: 0.7832 (ptp) REVERT: M 395 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6919 (mt-10) REVERT: N 107 LYS cc_start: 0.8345 (mmtp) cc_final: 0.7929 (ttpt) REVERT: N 117 LYS cc_start: 0.7849 (mmtp) cc_final: 0.7455 (mmmt) REVERT: N 187 TRP cc_start: 0.6524 (m100) cc_final: 0.6276 (m100) REVERT: N 291 ILE cc_start: 0.8090 (mm) cc_final: 0.7788 (mt) REVERT: N 295 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7849 (m-40) REVERT: N 375 GLU cc_start: 0.8069 (pt0) cc_final: 0.7761 (pm20) REVERT: N 512 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7637 (mm) outliers start: 65 outliers final: 28 residues processed: 424 average time/residue: 0.4607 time to fit residues: 293.1194 Evaluate side-chains 368 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 337 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 512 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 70.0000 chunk 201 optimal weight: 50.0000 chunk 164 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 38 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 113 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1165 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN N 268 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 27486 Z= 0.535 Angle : 0.713 8.686 38555 Z= 0.395 Chirality : 0.046 0.217 4262 Planarity : 0.006 0.072 3721 Dihedral : 27.499 178.387 6332 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.19 % Allowed : 17.89 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2335 helix: 0.18 (0.14), residues: 1272 sheet: -0.42 (0.48), residues: 121 loop : -0.82 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K1151 HIS 0.007 0.002 HIS L 38 PHE 0.022 0.003 PHE E 67 TYR 0.048 0.003 TYR A 54 ARG 0.007 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 386 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7930 (t70) cc_final: 0.7533 (t-90) REVERT: A 74 ILE cc_start: 0.7802 (tp) cc_final: 0.7595 (tt) REVERT: A 94 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: B 91 LYS cc_start: 0.5650 (tttp) cc_final: 0.5371 (tttm) REVERT: C 20 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7190 (ttm-80) REVERT: C 41 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 73 ASN cc_start: 0.6848 (t0) cc_final: 0.6430 (t0) REVERT: D 31 LYS cc_start: 0.8373 (mttt) cc_final: 0.7854 (pttt) REVERT: D 56 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6342 (tpp) REVERT: D 65 ASP cc_start: 0.7377 (t0) cc_final: 0.6933 (t0) REVERT: D 68 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6276 (mt-10) REVERT: D 79 HIS cc_start: 0.7096 (t-90) cc_final: 0.6657 (m170) REVERT: D 82 LYS cc_start: 0.7915 (tppt) cc_final: 0.7685 (mtmt) REVERT: E 41 TYR cc_start: 0.7441 (m-80) cc_final: 0.7240 (m-80) REVERT: E 42 ARG cc_start: 0.6504 (mtp85) cc_final: 0.6073 (mtt-85) REVERT: E 115 LYS cc_start: 0.7541 (mmmm) cc_final: 0.7247 (mptt) REVERT: F 77 LYS cc_start: 0.7450 (mttt) cc_final: 0.7011 (mmtp) REVERT: F 79 LYS cc_start: 0.6793 (mttp) cc_final: 0.6264 (mmtm) REVERT: G 41 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6839 (mt-10) REVERT: G 74 LYS cc_start: 0.6781 (tppt) cc_final: 0.6477 (mtpp) REVERT: G 104 GLN cc_start: 0.7037 (mt0) cc_final: 0.6279 (mm110) REVERT: H 52 SER cc_start: 0.7757 (t) cc_final: 0.7336 (p) REVERT: H 83 ARG cc_start: 0.6949 (mmt90) cc_final: 0.6690 (mmp80) REVERT: H 84 SER cc_start: 0.6155 (m) cc_final: 0.5827 (t) REVERT: H 90 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: K 841 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5385 (ptt) REVERT: K 860 MET cc_start: 0.8229 (mmt) cc_final: 0.7911 (mmm) REVERT: K 877 PHE cc_start: 0.7457 (m-80) cc_final: 0.7226 (m-80) REVERT: K 957 VAL cc_start: 0.8758 (t) cc_final: 0.8539 (t) REVERT: K 1182 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8004 (mttt) REVERT: K 1268 LEU cc_start: 0.8683 (mt) cc_final: 0.8291 (mt) REVERT: K 1317 ILE cc_start: 0.8071 (pt) cc_final: 0.7836 (mt) REVERT: K 1320 ASP cc_start: 0.7446 (t0) cc_final: 0.7224 (t0) REVERT: L 61 MET cc_start: 0.8217 (ptp) cc_final: 0.7920 (ptp) REVERT: L 88 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7652 (mtp-110) REVERT: L 105 ASN cc_start: 0.8001 (t0) cc_final: 0.7730 (t0) REVERT: L 247 TYR cc_start: 0.8470 (t80) cc_final: 0.8205 (t80) REVERT: L 288 MET cc_start: 0.8456 (ttp) cc_final: 0.8220 (ttp) REVERT: L 336 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7478 (mttt) REVERT: M 242 ASP cc_start: 0.8552 (m-30) cc_final: 0.8194 (m-30) REVERT: M 263 HIS cc_start: 0.7616 (t70) cc_final: 0.7250 (m-70) REVERT: M 308 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7361 (mm-30) REVERT: M 311 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7872 (mttm) REVERT: N 107 LYS cc_start: 0.8450 (mmtp) cc_final: 0.7840 (ttpt) REVERT: N 260 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7470 (mt-10) REVERT: N 331 ASN cc_start: 0.6774 (t0) cc_final: 0.6519 (t0) REVERT: N 466 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7784 (p) outliers start: 88 outliers final: 46 residues processed: 446 average time/residue: 0.4379 time to fit residues: 294.0619 Evaluate side-chains 388 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 336 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 841 MET Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 265 SER Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 325 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 407 ILE Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 466 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 779 ASN K1150 HIS ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 293 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 ASN M 353 GLN N 268 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27486 Z= 0.203 Angle : 0.531 7.160 38555 Z= 0.305 Chirality : 0.037 0.154 4262 Planarity : 0.004 0.058 3721 Dihedral : 26.857 177.860 6332 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.85 % Allowed : 19.27 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2335 helix: 0.77 (0.15), residues: 1278 sheet: -0.52 (0.51), residues: 107 loop : -0.60 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1151 HIS 0.004 0.001 HIS K1150 PHE 0.017 0.001 PHE K 723 TYR 0.023 0.001 TYR A 54 ARG 0.007 0.000 ARG M 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7819 (t70) cc_final: 0.7345 (t-90) REVERT: A 74 ILE cc_start: 0.7954 (tp) cc_final: 0.7748 (tt) REVERT: A 87 SER cc_start: 0.7021 (m) cc_final: 0.6477 (p) REVERT: B 91 LYS cc_start: 0.5846 (tttp) cc_final: 0.5530 (tttm) REVERT: B 93 GLN cc_start: 0.5103 (mm-40) cc_final: 0.4572 (mp10) REVERT: C 20 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7218 (ttm-80) REVERT: C 73 ASN cc_start: 0.6815 (t0) cc_final: 0.6393 (t0) REVERT: C 92 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7169 (mm-30) REVERT: D 31 LYS cc_start: 0.8366 (mttt) cc_final: 0.7871 (pttt) REVERT: D 48 ASP cc_start: 0.8184 (t70) cc_final: 0.7976 (t0) REVERT: D 56 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6505 (tpp) REVERT: D 68 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6195 (mt-10) REVERT: D 79 HIS cc_start: 0.6888 (t-90) cc_final: 0.6428 (m170) REVERT: D 82 LYS cc_start: 0.8103 (tppt) cc_final: 0.7856 (mppt) REVERT: E 42 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6299 (mtt-85) REVERT: E 79 LYS cc_start: 0.6666 (tttp) cc_final: 0.6370 (tttp) REVERT: E 90 MET cc_start: 0.5844 (mmm) cc_final: 0.5450 (mmp) REVERT: F 77 LYS cc_start: 0.7391 (mttt) cc_final: 0.6899 (mmtp) REVERT: F 79 LYS cc_start: 0.6893 (mttp) cc_final: 0.6271 (mmtm) REVERT: F 84 MET cc_start: 0.5363 (tpp) cc_final: 0.5082 (mmm) REVERT: H 81 ASN cc_start: 0.8069 (m110) cc_final: 0.7838 (m-40) REVERT: H 83 ARG cc_start: 0.6764 (mmt90) cc_final: 0.6542 (mmp80) REVERT: H 84 SER cc_start: 0.5995 (m) cc_final: 0.5777 (t) REVERT: K 668 PHE cc_start: 0.8056 (t80) cc_final: 0.7785 (t80) REVERT: K 726 TYR cc_start: 0.7255 (t80) cc_final: 0.6976 (t80) REVERT: K 779 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7799 (t0) REVERT: K 885 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6908 (pt0) REVERT: K 957 VAL cc_start: 0.8693 (t) cc_final: 0.8473 (t) REVERT: K 1164 MET cc_start: 0.8573 (ptt) cc_final: 0.8246 (ptt) REVERT: K 1268 LEU cc_start: 0.8649 (mt) cc_final: 0.8259 (mt) REVERT: L 53 MET cc_start: 0.8787 (mmp) cc_final: 0.8324 (mmm) REVERT: L 88 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7553 (mtp-110) REVERT: L 99 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7186 (ttt90) REVERT: L 105 ASN cc_start: 0.7925 (t0) cc_final: 0.7386 (t0) REVERT: L 133 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8150 (mtp85) REVERT: L 345 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7801 (mm-30) REVERT: L 367 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: M 37 MET cc_start: 0.2501 (tmm) cc_final: 0.2236 (tmm) REVERT: M 223 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7374 (tm-30) REVERT: M 242 ASP cc_start: 0.8523 (m-30) cc_final: 0.8217 (m-30) REVERT: M 280 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: N 107 LYS cc_start: 0.8417 (mmtp) cc_final: 0.7817 (ttpt) REVERT: N 126 GLU cc_start: 0.7313 (pm20) cc_final: 0.6926 (pm20) REVERT: N 260 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7392 (mt-10) REVERT: N 271 SER cc_start: 0.8921 (t) cc_final: 0.8632 (m) REVERT: N 331 ASN cc_start: 0.6441 (t0) cc_final: 0.6153 (t0) outliers start: 60 outliers final: 37 residues processed: 385 average time/residue: 0.4422 time to fit residues: 256.7658 Evaluate side-chains 367 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 326 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 779 ASN Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN K 722 ASN K 779 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN M 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27486 Z= 0.189 Angle : 0.514 7.917 38555 Z= 0.295 Chirality : 0.036 0.158 4262 Planarity : 0.004 0.051 3721 Dihedral : 26.681 177.458 6332 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.00 % Allowed : 19.98 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2335 helix: 1.10 (0.15), residues: 1278 sheet: -0.52 (0.51), residues: 107 loop : -0.43 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1151 HIS 0.004 0.001 HIS K1150 PHE 0.015 0.001 PHE L 160 TYR 0.021 0.001 TYR A 54 ARG 0.003 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 348 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7841 (t70) cc_final: 0.7447 (t-90) REVERT: A 74 ILE cc_start: 0.7885 (tp) cc_final: 0.7511 (tp) REVERT: A 87 SER cc_start: 0.6989 (m) cc_final: 0.6467 (p) REVERT: B 91 LYS cc_start: 0.5797 (tttp) cc_final: 0.5496 (tttm) REVERT: C 20 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7324 (ttm-80) REVERT: C 73 ASN cc_start: 0.6917 (t0) cc_final: 0.6486 (t0) REVERT: C 92 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7223 (mm-30) REVERT: C 104 GLN cc_start: 0.7430 (tt0) cc_final: 0.7209 (tt0) REVERT: D 31 LYS cc_start: 0.8367 (mttt) cc_final: 0.7859 (pttt) REVERT: D 56 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6467 (tpp) REVERT: D 65 ASP cc_start: 0.7344 (t0) cc_final: 0.6832 (t0) REVERT: D 68 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6309 (mt-10) REVERT: D 79 HIS cc_start: 0.6945 (t-90) cc_final: 0.6499 (m170) REVERT: D 81 ASN cc_start: 0.7650 (m-40) cc_final: 0.7073 (m110) REVERT: D 82 LYS cc_start: 0.8089 (tppt) cc_final: 0.7822 (mtmt) REVERT: E 42 ARG cc_start: 0.6502 (mtp85) cc_final: 0.5813 (mtm-85) REVERT: E 90 MET cc_start: 0.5873 (mmm) cc_final: 0.5396 (mmp) REVERT: F 77 LYS cc_start: 0.7311 (mttt) cc_final: 0.6833 (mmtp) REVERT: F 79 LYS cc_start: 0.6912 (mttp) cc_final: 0.6259 (mmtm) REVERT: F 84 MET cc_start: 0.5354 (tpp) cc_final: 0.5086 (mmm) REVERT: H 81 ASN cc_start: 0.7968 (m110) cc_final: 0.7688 (m-40) REVERT: K 668 PHE cc_start: 0.7992 (t80) cc_final: 0.7729 (t80) REVERT: K 727 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6660 (mp10) REVERT: K 841 MET cc_start: 0.5626 (ptt) cc_final: 0.5075 (ptt) REVERT: K 860 MET cc_start: 0.8076 (tpp) cc_final: 0.7822 (mmm) REVERT: K 885 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6874 (pt0) REVERT: K 957 VAL cc_start: 0.8687 (t) cc_final: 0.8479 (t) REVERT: K 1164 MET cc_start: 0.8507 (ptt) cc_final: 0.8243 (ptt) REVERT: K 1201 GLU cc_start: 0.7137 (mp0) cc_final: 0.6935 (mp0) REVERT: K 1268 LEU cc_start: 0.8610 (mt) cc_final: 0.8203 (mt) REVERT: L 51 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8057 (mp) REVERT: L 88 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7574 (mtp-110) REVERT: L 105 ASN cc_start: 0.7947 (t0) cc_final: 0.7435 (t0) REVERT: L 345 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7829 (mm-30) REVERT: M 37 MET cc_start: 0.2488 (tmm) cc_final: 0.2230 (tmm) REVERT: M 242 ASP cc_start: 0.8535 (m-30) cc_final: 0.8253 (m-30) REVERT: M 280 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: N 107 LYS cc_start: 0.8381 (mmtp) cc_final: 0.7806 (ttpt) REVERT: N 126 GLU cc_start: 0.7313 (pm20) cc_final: 0.6888 (pm20) REVERT: N 271 SER cc_start: 0.8882 (t) cc_final: 0.8603 (m) REVERT: N 331 ASN cc_start: 0.6255 (t0) cc_final: 0.5985 (t0) REVERT: N 375 GLU cc_start: 0.8146 (pt0) cc_final: 0.7628 (pm20) outliers start: 63 outliers final: 45 residues processed: 388 average time/residue: 0.4517 time to fit residues: 265.9449 Evaluate side-chains 375 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 327 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 265 SER Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN K 722 ASN L 38 HIS L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27486 Z= 0.253 Angle : 0.540 8.539 38555 Z= 0.307 Chirality : 0.038 0.204 4262 Planarity : 0.004 0.049 3721 Dihedral : 26.758 177.327 6332 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.47 % Allowed : 19.70 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2335 helix: 1.13 (0.15), residues: 1276 sheet: -0.55 (0.51), residues: 107 loop : -0.39 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1151 HIS 0.004 0.001 HIS K1150 PHE 0.017 0.001 PHE K 723 TYR 0.026 0.002 TYR A 54 ARG 0.010 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 336 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7890 (t70) cc_final: 0.7471 (t-90) REVERT: B 91 LYS cc_start: 0.5790 (tttp) cc_final: 0.5486 (tttm) REVERT: B 93 GLN cc_start: 0.5085 (mm-40) cc_final: 0.4496 (mp10) REVERT: C 20 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7335 (ttm-80) REVERT: C 73 ASN cc_start: 0.6924 (t0) cc_final: 0.6483 (t0) REVERT: C 92 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 31 LYS cc_start: 0.8326 (mttt) cc_final: 0.7839 (pttt) REVERT: D 56 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6514 (tpp) REVERT: D 65 ASP cc_start: 0.7385 (t0) cc_final: 0.6868 (t0) REVERT: D 68 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6325 (mt-10) REVERT: D 79 HIS cc_start: 0.6957 (t-90) cc_final: 0.6596 (m170) REVERT: D 82 LYS cc_start: 0.8102 (tppt) cc_final: 0.7832 (mtmt) REVERT: D 90 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6690 (mt-10) REVERT: E 41 TYR cc_start: 0.7511 (m-80) cc_final: 0.7293 (m-80) REVERT: E 42 ARG cc_start: 0.6524 (mtp85) cc_final: 0.5850 (mtm-85) REVERT: E 90 MET cc_start: 0.5918 (mmm) cc_final: 0.5392 (mmp) REVERT: F 77 LYS cc_start: 0.7266 (mttt) cc_final: 0.6820 (mmtp) REVERT: F 79 LYS cc_start: 0.6779 (mttp) cc_final: 0.6223 (mmtm) REVERT: F 84 MET cc_start: 0.5365 (tpp) cc_final: 0.5068 (mmm) REVERT: H 52 SER cc_start: 0.7878 (t) cc_final: 0.7339 (p) REVERT: H 83 ARG cc_start: 0.6908 (mpt180) cc_final: 0.6668 (mmp80) REVERT: K 841 MET cc_start: 0.5605 (ptt) cc_final: 0.5041 (ptt) REVERT: K 860 MET cc_start: 0.8079 (tpp) cc_final: 0.7814 (mmm) REVERT: K 885 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6877 (pt0) REVERT: K 957 VAL cc_start: 0.8710 (t) cc_final: 0.8501 (t) REVERT: K 1164 MET cc_start: 0.8546 (ptt) cc_final: 0.8174 (ptt) REVERT: K 1268 LEU cc_start: 0.8627 (mt) cc_final: 0.8199 (mt) REVERT: L 51 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (mp) REVERT: L 105 ASN cc_start: 0.7927 (t0) cc_final: 0.7463 (t0) REVERT: L 336 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7607 (mmtm) REVERT: L 345 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7859 (mm-30) REVERT: L 367 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: M 37 MET cc_start: 0.2481 (tmm) cc_final: 0.2236 (tmm) REVERT: M 242 ASP cc_start: 0.8546 (m-30) cc_final: 0.8272 (m-30) REVERT: M 280 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: N 107 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7719 (ttpt) REVERT: N 126 GLU cc_start: 0.7163 (pm20) cc_final: 0.6717 (pm20) REVERT: N 271 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8610 (m) REVERT: N 331 ASN cc_start: 0.6377 (t0) cc_final: 0.6083 (t0) REVERT: N 375 GLU cc_start: 0.8139 (pt0) cc_final: 0.7596 (pm20) REVERT: N 466 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7732 (p) REVERT: N 515 GLN cc_start: 0.7689 (mt0) cc_final: 0.7344 (pp30) outliers start: 73 outliers final: 52 residues processed: 384 average time/residue: 0.4083 time to fit residues: 238.7319 Evaluate side-chains 382 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 323 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 790 SER Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1194 MET Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 265 SER Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 466 CYS Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN K 779 ASN L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN N 421 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27486 Z= 0.178 Angle : 0.510 7.918 38555 Z= 0.293 Chirality : 0.036 0.185 4262 Planarity : 0.004 0.047 3721 Dihedral : 26.580 178.160 6332 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.14 % Allowed : 19.84 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2335 helix: 1.39 (0.15), residues: 1277 sheet: -0.50 (0.51), residues: 107 loop : -0.28 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1151 HIS 0.004 0.001 HIS K 998 PHE 0.020 0.001 PHE K 723 TYR 0.017 0.001 TYR A 54 ARG 0.009 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 343 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7847 (t70) cc_final: 0.7456 (t-90) REVERT: A 87 SER cc_start: 0.7009 (m) cc_final: 0.6493 (p) REVERT: B 91 LYS cc_start: 0.5789 (tttp) cc_final: 0.5529 (tttm) REVERT: C 20 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7525 (ttm-80) REVERT: C 73 ASN cc_start: 0.6908 (t0) cc_final: 0.6470 (t0) REVERT: C 92 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7222 (mm-30) REVERT: C 111 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5628 (mm) REVERT: D 31 LYS cc_start: 0.8330 (mttt) cc_final: 0.7841 (pttt) REVERT: D 56 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6502 (tpp) REVERT: D 65 ASP cc_start: 0.7354 (t0) cc_final: 0.6833 (t0) REVERT: D 68 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6340 (mt-10) REVERT: D 79 HIS cc_start: 0.6826 (t-90) cc_final: 0.6435 (m170) REVERT: D 82 LYS cc_start: 0.8098 (tppt) cc_final: 0.7828 (mtmt) REVERT: D 90 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6633 (mt-10) REVERT: E 42 ARG cc_start: 0.6525 (mtp85) cc_final: 0.5902 (mtm-85) REVERT: E 90 MET cc_start: 0.5940 (mmm) cc_final: 0.5647 (mmm) REVERT: F 77 LYS cc_start: 0.7228 (mttt) cc_final: 0.6782 (mmtp) REVERT: F 79 LYS cc_start: 0.6969 (mttp) cc_final: 0.6441 (mmtm) REVERT: F 84 MET cc_start: 0.5320 (tpp) cc_final: 0.5045 (mmm) REVERT: H 52 SER cc_start: 0.7743 (t) cc_final: 0.7134 (p) REVERT: H 83 ARG cc_start: 0.6918 (mpt180) cc_final: 0.6677 (mmp80) REVERT: K 668 PHE cc_start: 0.7953 (t80) cc_final: 0.7688 (t80) REVERT: K 841 MET cc_start: 0.5554 (ptt) cc_final: 0.5053 (ptt) REVERT: K 860 MET cc_start: 0.8027 (tpp) cc_final: 0.7766 (mmm) REVERT: K 877 PHE cc_start: 0.7304 (m-80) cc_final: 0.7059 (m-10) REVERT: K 885 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6857 (pt0) REVERT: K 957 VAL cc_start: 0.8684 (t) cc_final: 0.8470 (t) REVERT: K 1164 MET cc_start: 0.8523 (ptt) cc_final: 0.8219 (ptt) REVERT: K 1201 GLU cc_start: 0.7126 (mp0) cc_final: 0.6870 (mp0) REVERT: L 51 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8059 (mp) REVERT: L 99 ARG cc_start: 0.7514 (ttt90) cc_final: 0.7288 (ttt90) REVERT: L 105 ASN cc_start: 0.7920 (t0) cc_final: 0.7482 (t0) REVERT: L 345 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7774 (mm-30) REVERT: L 367 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: M 37 MET cc_start: 0.2466 (tmm) cc_final: 0.2224 (tmm) REVERT: M 242 ASP cc_start: 0.8541 (m-30) cc_final: 0.8283 (m-30) REVERT: M 280 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: M 361 ASP cc_start: 0.6617 (t0) cc_final: 0.6413 (t0) REVERT: N 107 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7601 (ttpt) REVERT: N 271 SER cc_start: 0.8865 (t) cc_final: 0.8609 (m) REVERT: N 331 ASN cc_start: 0.6451 (t0) cc_final: 0.6147 (t0) REVERT: N 375 GLU cc_start: 0.8090 (pt0) cc_final: 0.7567 (pm20) REVERT: N 421 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8243 (t0) REVERT: N 515 GLN cc_start: 0.7664 (mt0) cc_final: 0.7180 (pp30) REVERT: P 538 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8327 (pttt) outliers start: 66 outliers final: 47 residues processed: 384 average time/residue: 0.4347 time to fit residues: 252.6549 Evaluate side-chains 379 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 326 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 790 SER Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1293 HIS Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 421 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN N 421 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27486 Z= 0.290 Angle : 0.557 8.430 38555 Z= 0.315 Chirality : 0.038 0.170 4262 Planarity : 0.004 0.047 3721 Dihedral : 26.792 177.802 6332 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.66 % Allowed : 19.65 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2335 helix: 1.24 (0.15), residues: 1271 sheet: -0.43 (0.51), residues: 105 loop : -0.33 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.004 0.001 HIS L 38 PHE 0.016 0.002 PHE A 67 TYR 0.025 0.002 TYR A 54 ARG 0.008 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 337 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.5739 (tttp) cc_final: 0.5421 (tttm) REVERT: B 93 GLN cc_start: 0.5024 (mm110) cc_final: 0.4522 (mp10) REVERT: C 20 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7482 (ttm-80) REVERT: C 73 ASN cc_start: 0.6900 (t0) cc_final: 0.6457 (t0) REVERT: C 92 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 31 LYS cc_start: 0.8329 (mttt) cc_final: 0.7828 (pttt) REVERT: D 56 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6509 (tpp) REVERT: D 65 ASP cc_start: 0.7424 (t0) cc_final: 0.6914 (t0) REVERT: D 68 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6380 (mt-10) REVERT: D 79 HIS cc_start: 0.6880 (t-90) cc_final: 0.6585 (m170) REVERT: D 82 LYS cc_start: 0.8125 (tppt) cc_final: 0.7845 (mtmt) REVERT: D 90 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6566 (mt-10) REVERT: E 42 ARG cc_start: 0.6551 (mtp85) cc_final: 0.5985 (mtm-85) REVERT: E 90 MET cc_start: 0.5986 (mmm) cc_final: 0.5437 (mmp) REVERT: F 77 LYS cc_start: 0.7202 (mttt) cc_final: 0.6803 (mmtp) REVERT: F 79 LYS cc_start: 0.6890 (mttp) cc_final: 0.6275 (mmtm) REVERT: F 84 MET cc_start: 0.5448 (tpp) cc_final: 0.5149 (mmm) REVERT: H 52 SER cc_start: 0.7784 (t) cc_final: 0.7283 (p) REVERT: H 65 ASP cc_start: 0.5677 (t70) cc_final: 0.5429 (t0) REVERT: H 83 ARG cc_start: 0.6980 (mpt180) cc_final: 0.6755 (mmp80) REVERT: H 90 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: K 841 MET cc_start: 0.5741 (ptt) cc_final: 0.5156 (ptt) REVERT: K 860 MET cc_start: 0.8005 (tpp) cc_final: 0.7756 (mmm) REVERT: K 885 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6870 (pt0) REVERT: K 957 VAL cc_start: 0.8722 (t) cc_final: 0.8504 (t) REVERT: L 51 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8081 (mp) REVERT: L 99 ARG cc_start: 0.7567 (ttt90) cc_final: 0.7255 (ttt90) REVERT: L 105 ASN cc_start: 0.7956 (t0) cc_final: 0.7513 (t0) REVERT: L 336 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7646 (mmtm) REVERT: L 345 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7890 (mm-30) REVERT: L 367 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: M 37 MET cc_start: 0.2467 (tmm) cc_final: 0.2226 (tmm) REVERT: M 242 ASP cc_start: 0.8545 (m-30) cc_final: 0.8290 (m-30) REVERT: M 280 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: M 308 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7333 (mt-10) REVERT: N 107 LYS cc_start: 0.8249 (mmtp) cc_final: 0.7606 (ttpt) REVERT: N 271 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8609 (m) REVERT: N 331 ASN cc_start: 0.6338 (t0) cc_final: 0.6025 (t0) REVERT: N 375 GLU cc_start: 0.8109 (pt0) cc_final: 0.7550 (pm20) REVERT: N 385 GLN cc_start: 0.7077 (mt0) cc_final: 0.6737 (mt0) REVERT: N 421 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8253 (t0) REVERT: N 466 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7732 (p) REVERT: P 538 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8357 (pttt) outliers start: 77 outliers final: 55 residues processed: 385 average time/residue: 0.4431 time to fit residues: 259.3180 Evaluate side-chains 392 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 328 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 790 SER Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1194 MET Chi-restraints excluded: chain K residue 1228 LEU Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1293 HIS Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 265 SER Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 421 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 466 CYS Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.5980 chunk 245 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 143 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN L 93 ASN L 135 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27486 Z= 0.177 Angle : 0.515 7.220 38555 Z= 0.296 Chirality : 0.036 0.198 4262 Planarity : 0.004 0.046 3721 Dihedral : 26.604 178.556 6332 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.00 % Allowed : 20.55 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2335 helix: 1.50 (0.15), residues: 1268 sheet: -0.46 (0.51), residues: 107 loop : -0.22 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1151 HIS 0.004 0.001 HIS L 38 PHE 0.012 0.001 PHE A 67 TYR 0.017 0.001 TYR A 54 ARG 0.008 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 331 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.5843 (tttp) cc_final: 0.5517 (tttm) REVERT: C 20 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7536 (ttm-80) REVERT: C 92 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 31 LYS cc_start: 0.8324 (mttt) cc_final: 0.7822 (pttt) REVERT: D 56 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6476 (tpp) REVERT: D 65 ASP cc_start: 0.7358 (t0) cc_final: 0.6848 (t0) REVERT: D 68 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6344 (mt-10) REVERT: D 79 HIS cc_start: 0.6781 (t-90) cc_final: 0.6420 (m170) REVERT: D 82 LYS cc_start: 0.8109 (tppt) cc_final: 0.7880 (mppt) REVERT: D 90 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6518 (mt-10) REVERT: E 42 ARG cc_start: 0.6524 (mtp85) cc_final: 0.5997 (mtm-85) REVERT: E 90 MET cc_start: 0.5965 (mmm) cc_final: 0.5647 (mmm) REVERT: F 77 LYS cc_start: 0.7182 (mttt) cc_final: 0.6769 (mmtp) REVERT: F 79 LYS cc_start: 0.6967 (mttp) cc_final: 0.6419 (mmtm) REVERT: F 84 MET cc_start: 0.5299 (tpp) cc_final: 0.5027 (mmm) REVERT: G 33 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4714 (mm) REVERT: H 52 SER cc_start: 0.7623 (t) cc_final: 0.7142 (p) REVERT: H 65 ASP cc_start: 0.5598 (t70) cc_final: 0.5348 (t0) REVERT: H 83 ARG cc_start: 0.6939 (mpt180) cc_final: 0.6696 (mmp80) REVERT: H 90 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: K 668 PHE cc_start: 0.7959 (t80) cc_final: 0.7679 (t80) REVERT: K 841 MET cc_start: 0.5579 (ptt) cc_final: 0.5069 (ptt) REVERT: K 860 MET cc_start: 0.8026 (tpp) cc_final: 0.7775 (mmm) REVERT: K 885 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6853 (pt0) REVERT: K 957 VAL cc_start: 0.8697 (t) cc_final: 0.8477 (t) REVERT: L 51 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8078 (mp) REVERT: L 99 ARG cc_start: 0.7520 (ttt90) cc_final: 0.7258 (ttt90) REVERT: L 105 ASN cc_start: 0.7941 (t0) cc_final: 0.7479 (t0) REVERT: L 288 MET cc_start: 0.8438 (ttp) cc_final: 0.8219 (ttp) REVERT: L 336 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7480 (mmtm) REVERT: L 345 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7829 (mm-30) REVERT: L 367 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: M 37 MET cc_start: 0.2454 (tmm) cc_final: 0.2231 (tmm) REVERT: M 242 ASP cc_start: 0.8538 (m-30) cc_final: 0.8294 (m-30) REVERT: M 280 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: M 324 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7514 (mtt90) REVERT: N 107 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7672 (ttpt) REVERT: N 271 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8599 (m) REVERT: N 375 GLU cc_start: 0.8101 (pt0) cc_final: 0.7579 (pm20) REVERT: N 385 GLN cc_start: 0.7016 (mt0) cc_final: 0.6702 (mt0) REVERT: N 466 CYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7716 (p) REVERT: P 538 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8349 (pttt) outliers start: 63 outliers final: 49 residues processed: 368 average time/residue: 0.4601 time to fit residues: 254.4114 Evaluate side-chains 378 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 790 SER Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1194 MET Chi-restraints excluded: chain K residue 1228 LEU Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1293 HIS Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 466 CYS Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27486 Z= 0.176 Angle : 0.514 9.643 38555 Z= 0.294 Chirality : 0.036 0.172 4262 Planarity : 0.004 0.045 3721 Dihedral : 26.538 178.628 6332 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.09 % Allowed : 20.50 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2335 helix: 1.64 (0.15), residues: 1269 sheet: -0.37 (0.52), residues: 105 loop : -0.14 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1151 HIS 0.003 0.001 HIS K 998 PHE 0.020 0.001 PHE K1022 TYR 0.016 0.001 TYR A 54 ARG 0.008 0.000 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 331 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.5866 (tttp) cc_final: 0.5538 (tttm) REVERT: B 93 GLN cc_start: 0.4939 (mm110) cc_final: 0.4342 (mp10) REVERT: C 20 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7568 (ttm-80) REVERT: C 92 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7220 (mm-30) REVERT: D 31 LYS cc_start: 0.8339 (mttt) cc_final: 0.7831 (pttt) REVERT: D 56 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6468 (tpp) REVERT: D 65 ASP cc_start: 0.7358 (t0) cc_final: 0.6834 (t0) REVERT: D 68 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6361 (mt-10) REVERT: D 79 HIS cc_start: 0.6816 (t-90) cc_final: 0.6437 (m170) REVERT: E 42 ARG cc_start: 0.6645 (mtp85) cc_final: 0.6082 (mtm-85) REVERT: E 90 MET cc_start: 0.5943 (mmm) cc_final: 0.5623 (mmm) REVERT: F 44 LYS cc_start: 0.8057 (tttt) cc_final: 0.7722 (tttt) REVERT: F 77 LYS cc_start: 0.7183 (mttt) cc_final: 0.6757 (mmtp) REVERT: F 79 LYS cc_start: 0.6970 (mttp) cc_final: 0.6420 (mmtm) REVERT: F 84 MET cc_start: 0.5300 (tpp) cc_final: 0.5023 (mmm) REVERT: G 33 LEU cc_start: 0.5009 (OUTLIER) cc_final: 0.4635 (mm) REVERT: G 74 LYS cc_start: 0.6788 (tppt) cc_final: 0.6574 (mmmm) REVERT: H 52 SER cc_start: 0.7589 (t) cc_final: 0.7140 (p) REVERT: H 65 ASP cc_start: 0.5682 (t70) cc_final: 0.5426 (t0) REVERT: H 83 ARG cc_start: 0.6915 (mpt180) cc_final: 0.6668 (mmp80) REVERT: K 668 PHE cc_start: 0.7912 (t80) cc_final: 0.7634 (t80) REVERT: K 841 MET cc_start: 0.5554 (ptt) cc_final: 0.5055 (ptt) REVERT: K 860 MET cc_start: 0.7960 (tpp) cc_final: 0.7716 (mmm) REVERT: K 885 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6834 (pt0) REVERT: K 957 VAL cc_start: 0.8695 (t) cc_final: 0.8480 (t) REVERT: K 1201 GLU cc_start: 0.7113 (mp0) cc_final: 0.6860 (mp0) REVERT: L 51 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (mp) REVERT: L 99 ARG cc_start: 0.7527 (ttt90) cc_final: 0.7263 (ttt90) REVERT: L 105 ASN cc_start: 0.7943 (t0) cc_final: 0.7525 (t0) REVERT: L 156 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6873 (pt0) REVERT: L 288 MET cc_start: 0.8454 (ttp) cc_final: 0.8227 (ttp) REVERT: L 345 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7822 (mm-30) REVERT: L 367 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: M 37 MET cc_start: 0.2353 (tmm) cc_final: 0.2132 (tmm) REVERT: M 242 ASP cc_start: 0.8549 (m-30) cc_final: 0.8310 (m-30) REVERT: M 280 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: M 324 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7526 (mtt90) REVERT: N 107 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7688 (ttpt) REVERT: N 375 GLU cc_start: 0.8075 (pt0) cc_final: 0.7563 (pm20) REVERT: N 466 CYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7698 (p) REVERT: P 538 LYS cc_start: 0.8577 (ptpt) cc_final: 0.8342 (pttt) outliers start: 65 outliers final: 49 residues processed: 368 average time/residue: 0.4497 time to fit residues: 249.5772 Evaluate side-chains 378 residues out of total 2102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 322 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 722 ASN Chi-restraints excluded: chain K residue 790 SER Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1194 MET Chi-restraints excluded: chain K residue 1228 LEU Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain K residue 1293 HIS Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 466 CYS Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 64 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN L 93 ASN L 135 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121216 restraints weight = 31961.808| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.11 r_work: 0.3217 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27486 Z= 0.313 Angle : 0.577 9.987 38555 Z= 0.324 Chirality : 0.039 0.182 4262 Planarity : 0.004 0.046 3721 Dihedral : 26.809 178.033 6332 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.95 % Allowed : 20.46 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2335 helix: 1.28 (0.15), residues: 1277 sheet: -0.39 (0.52), residues: 105 loop : -0.27 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.006 0.001 HIS L 38 PHE 0.043 0.002 PHE K1022 TYR 0.025 0.002 TYR A 54 ARG 0.009 0.001 ARG L 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.09 seconds wall clock time: 119 minutes 44.72 seconds (7184.72 seconds total)