Starting phenix.real_space_refine on Sat Feb 17 09:33:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plm_13493/02_2024/7plm_13493_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 24 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 145 5.16 5 C 11424 2.51 5 N 3078 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 874": "OE1" <-> "OE2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18225 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 bond proxies already assigned to first conformer: 9174 Chain: "B" Number of atoms: 9005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 bond proxies already assigned to first conformer: 9170 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {' CA': 1, ' MG': 1, 'SF4': 3, 'TPP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {' CA': 1, ' MG': 1, 'SF4': 3, 'TPP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5544 SG CYS A 755 81.996 27.505 78.240 1.00 39.15 S ATOM 5127 SG CYS A 695 77.454 27.520 73.988 1.00 28.18 S ATOM 5098 SG ACYS A 692 75.981 28.432 79.862 0.50 16.14 S ATOM 5075 SG CYS A 689 77.888 22.405 78.212 1.00 19.33 S ATOM 5517 SG CYS A 751 82.062 30.513 70.769 1.00 10.27 S ATOM 5156 SG CYS A 699 77.767 32.048 66.797 1.00 7.85 S ATOM 5481 SG CYS A 745 83.607 29.890 64.453 1.00 13.08 S ATOM 5499 SG CYS A 748 82.408 35.798 67.548 1.00 12.03 S ATOM 6197 SG CYS A 840 76.727 47.644 59.041 1.00 31.03 S ATOM 5988 SG CYS A 812 81.818 43.969 59.819 1.00 20.30 S ATOM 6004 SG CYS A 815 76.751 42.993 63.616 1.00 12.97 S ATOM 7912 SG CYS A1071 80.527 48.775 63.306 1.00 17.38 S ATOM 14546 SG CYS B 755 42.062 100.160 78.236 1.00 42.28 S ATOM 14129 SG CYS B 695 46.567 100.182 73.962 1.00 30.47 S ATOM 14100 SG ACYS B 692 48.078 99.224 79.862 0.50 14.76 S ATOM 14077 SG CYS B 689 46.178 105.253 78.212 1.00 20.78 S ATOM 14519 SG CYS B 751 41.993 97.148 70.767 1.00 9.78 S ATOM 14158 SG CYS B 699 46.291 95.625 66.795 1.00 7.42 S ATOM 14483 SG CYS B 745 40.454 97.772 64.454 1.00 10.82 S ATOM 14501 SG CYS B 748 41.650 91.859 67.546 1.00 11.41 S ATOM 15199 SG CYS B 840 47.333 80.010 59.037 1.00 29.38 S ATOM 14990 SG CYS B 812 42.245 83.689 59.819 1.00 21.48 S ATOM 15006 SG CYS B 815 47.311 84.665 63.614 1.00 12.97 S ATOM 16914 SG CYS B1071 43.538 78.883 63.307 1.00 20.63 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS A 692 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 692 " occ=0.50 residue: pdb=" N ACYS B 692 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 692 " occ=0.50 Time building chain proxies: 16.18, per 1000 atoms: 0.89 Number of scatterers: 18225 At special positions: 0 Unit cell: (124.961, 128.557, 100.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 24 26.01 Ca 2 19.99 S 145 16.00 P 4 15.00 Mg 2 11.99 O 3546 8.00 N 3078 7.00 C 11424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1212 " distance=2.04 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG ACYS B1212 " distance=2.04 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: 6.70 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG ACYS A 692 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 689 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 755 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 695 " pdb=" SF4 A1302 " pdb="FE3 SF4 A1302 " - pdb=" SG CYS A 745 " pdb="FE4 SF4 A1302 " - pdb=" SG CYS A 748 " pdb="FE2 SF4 A1302 " - pdb=" SG CYS A 699 " pdb="FE1 SF4 A1302 " - pdb=" SG CYS A 751 " pdb=" SF4 A1303 " pdb="FE4 SF4 A1303 " - pdb=" SG CYS A1071 " pdb="FE1 SF4 A1303 " - pdb=" SG CYS A 840 " pdb="FE2 SF4 A1303 " - pdb=" SG CYS A 812 " pdb="FE3 SF4 A1303 " - pdb=" SG CYS A 815 " pdb=" SF4 B1301 " pdb="FE3 SF4 B1301 " - pdb=" SG ACYS B 692 " pdb="FE4 SF4 B1301 " - pdb=" SG CYS B 689 " pdb="FE1 SF4 B1301 " - pdb=" SG CYS B 755 " pdb="FE2 SF4 B1301 " - pdb=" SG CYS B 695 " pdb=" SF4 B1302 " pdb="FE3 SF4 B1302 " - pdb=" SG CYS B 745 " pdb="FE4 SF4 B1302 " - pdb=" SG CYS B 748 " pdb="FE2 SF4 B1302 " - pdb=" SG CYS B 699 " pdb="FE1 SF4 B1302 " - pdb=" SG CYS B 751 " pdb=" SF4 B1303 " pdb="FE4 SF4 B1303 " - pdb=" SG CYS B1071 " pdb="FE2 SF4 B1303 " - pdb=" SG CYS B 812 " pdb="FE1 SF4 B1303 " - pdb=" SG CYS B 840 " pdb="FE3 SF4 B1303 " - pdb=" SG CYS B 815 " Number of angles added : 72 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 16 sheets defined 41.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.624A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 87 through 102 Proline residue: A 95 - end of helix removed outlier: 3.679A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 removed outlier: 3.658A pdb=" N ALA A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.523A pdb=" N SER A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 225 through 254 removed outlier: 4.752A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Proline residue: A 234 - end of helix Proline residue: A 240 - end of helix removed outlier: 3.633A pdb=" N LEU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 293 removed outlier: 3.935A pdb=" N ILE A 283 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 291 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.637A pdb=" N GLY A 496 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 694 through 698 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 775 through 783 removed outlier: 4.586A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 828 Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 872 through 897 Processing helix chain 'A' and resid 904 through 915 Processing helix chain 'A' and resid 920 through 933 Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 963 through 967 Processing helix chain 'A' and resid 971 through 977 Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 3.637A pdb=" N THR A1031 " --> pdb=" O ARG A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1072 through 1074 No H-bonds generated for 'chain 'A' and resid 1072 through 1074' Processing helix chain 'A' and resid 1080 through 1092 removed outlier: 4.651A pdb=" N GLN A1084 " --> pdb=" O GLY A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1132 through 1140 Processing helix chain 'A' and resid 1142 through 1167 Processing helix chain 'A' and resid 1201 through 1203 No H-bonds generated for 'chain 'A' and resid 1201 through 1203' Processing helix chain 'A' and resid 1220 through 1229 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.620A pdb=" N VAL B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 87 through 102 Proline residue: B 95 - end of helix removed outlier: 3.672A pdb=" N LYS B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 removed outlier: 3.654A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 163 Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.530A pdb=" N SER B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 225 through 254 removed outlier: 4.745A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Proline residue: B 234 - end of helix Proline residue: B 240 - end of helix removed outlier: 3.649A pdb=" N LEU B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.935A pdb=" N ILE B 283 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 291 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 430 through 444 Processing helix chain 'B' and resid 492 through 497 removed outlier: 3.649A pdb=" N GLY B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 528 through 536 Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 580 through 589 Processing helix chain 'B' and resid 599 through 612 Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 651 through 653 No H-bonds generated for 'chain 'B' and resid 651 through 653' Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 694 through 698 Processing helix chain 'B' and resid 750 through 754 Processing helix chain 'B' and resid 775 through 783 removed outlier: 4.592A pdb=" N ARG B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 818 through 828 Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 872 through 897 Processing helix chain 'B' and resid 904 through 915 Processing helix chain 'B' and resid 920 through 933 Processing helix chain 'B' and resid 940 through 947 Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 963 through 967 Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 1025 through 1031 removed outlier: 3.634A pdb=" N THR B1031 " --> pdb=" O ARG B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1057 Processing helix chain 'B' and resid 1072 through 1074 No H-bonds generated for 'chain 'B' and resid 1072 through 1074' Processing helix chain 'B' and resid 1080 through 1092 removed outlier: 4.652A pdb=" N GLN B1084 " --> pdb=" O GLY B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1129 Processing helix chain 'B' and resid 1132 through 1140 Processing helix chain 'B' and resid 1142 through 1167 Processing helix chain 'B' and resid 1201 through 1203 No H-bonds generated for 'chain 'B' and resid 1201 through 1203' Processing helix chain 'B' and resid 1220 through 1229 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.311A pdb=" N THR A 57 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 27 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG A 59 " --> pdb=" O ILE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 82 through 85 removed outlier: 6.708A pdb=" N VAL A 108 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR A 85 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A 110 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A 167 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 111 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS A 169 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA A 113 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 171 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A 139 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 170 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 141 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASP A 172 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N SER A 143 " --> pdb=" O ASP A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.559A pdb=" N ARG A 271 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 300 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 273 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 302 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 275 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 323 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 274 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR A 325 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS A 357 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 326 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 359 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP A 328 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY A 361 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 390 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 540 through 544 Processing sheet with id= F, first strand: chain 'A' and resid 680 through 684 Processing sheet with id= G, first strand: chain 'A' and resid 704 through 710 Processing sheet with id= H, first strand: chain 'A' and resid 863 through 866 removed outlier: 6.436A pdb=" N SER A 956 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 835 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 958 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 985 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY A 961 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 987 " --> pdb=" O GLY A 961 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A1063 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 988 " --> pdb=" O SER A1063 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A1065 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP A 990 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A1067 " --> pdb=" O ASP A 990 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A1099 " --> pdb=" O THR A1039 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.309A pdb=" N THR B 57 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE B 27 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 59 " --> pdb=" O ILE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 82 through 85 removed outlier: 6.706A pdb=" N VAL B 108 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR B 85 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS B 110 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 167 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 111 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS B 169 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA B 113 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE B 171 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 139 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 170 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 141 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ASP B 172 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N SER B 143 " --> pdb=" O ASP B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 261 through 265 removed outlier: 6.552A pdb=" N ARG B 271 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 300 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 273 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 302 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER B 275 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 323 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL B 274 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 325 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS B 357 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 326 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 359 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP B 328 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B 361 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 390 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 540 through 544 Processing sheet with id= N, first strand: chain 'B' and resid 680 through 684 Processing sheet with id= O, first strand: chain 'B' and resid 704 through 710 Processing sheet with id= P, first strand: chain 'B' and resid 863 through 866 removed outlier: 6.442A pdb=" N SER B 956 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA B 835 " --> pdb=" O SER B 956 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP B 958 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B 985 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY B 961 " --> pdb=" O ASN B 985 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE B 987 " --> pdb=" O GLY B 961 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B1063 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 988 " --> pdb=" O SER B1063 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 990 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA B1067 " --> pdb=" O ASP B 990 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B1099 " --> pdb=" O THR B1039 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 7804 1.43 - 1.65: 10427 1.65 - 1.86: 203 1.86 - 2.07: 0 2.07 - 2.29: 72 Bond restraints: 18506 Sorted by residual: bond pdb=" C PHE A 174 " pdb=" N ARG A 175 " ideal model delta sigma weight residual 1.332 1.304 0.029 1.40e-02 5.10e+03 4.21e+00 bond pdb=" C PHE B 174 " pdb=" N ARG B 175 " ideal model delta sigma weight residual 1.332 1.306 0.027 1.40e-02 5.10e+03 3.65e+00 bond pdb=" O3B TPP B1304 " pdb=" PB TPP B1304 " ideal model delta sigma weight residual 1.532 1.485 0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" O3B TPP A1304 " pdb=" PB TPP A1304 " ideal model delta sigma weight residual 1.532 1.485 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB THR A 112 " pdb=" CG2 THR A 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 ... (remaining 18501 not shown) Histogram of bond angle deviations from ideal: 73.35 - 86.63: 72 86.63 - 99.91: 10 99.91 - 113.19: 10393 113.19 - 126.47: 14346 126.47 - 139.75: 234 Bond angle restraints: 25055 Sorted by residual: angle pdb=" O3A TPP B1304 " pdb=" PB TPP B1304 " pdb=" O3B TPP B1304 " ideal model delta sigma weight residual 104.26 110.51 -6.25 1.33e+00 5.64e-01 2.20e+01 angle pdb=" O3A TPP A1304 " pdb=" PB TPP A1304 " pdb=" O3B TPP A1304 " ideal model delta sigma weight residual 104.26 110.47 -6.21 1.33e+00 5.64e-01 2.17e+01 angle pdb=" O1B TPP A1304 " pdb=" PB TPP A1304 " pdb=" O3A TPP A1304 " ideal model delta sigma weight residual 111.16 104.34 6.82 1.82e+00 3.03e-01 1.41e+01 angle pdb=" O1B TPP B1304 " pdb=" PB TPP B1304 " pdb=" O3A TPP B1304 " ideal model delta sigma weight residual 111.16 104.34 6.82 1.82e+00 3.03e-01 1.41e+01 angle pdb=" CA TRP A 844 " pdb=" CB TRP A 844 " pdb=" CG TRP A 844 " ideal model delta sigma weight residual 113.60 119.79 -6.19 1.90e+00 2.77e-01 1.06e+01 ... (remaining 25050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9985 17.94 - 35.87: 829 35.87 - 53.81: 184 53.81 - 71.74: 42 71.74 - 89.68: 15 Dihedral angle restraints: 11055 sinusoidal: 4327 harmonic: 6728 Sorted by residual: dihedral pdb=" CA PHE B 124 " pdb=" C PHE B 124 " pdb=" N GLY B 125 " pdb=" CA GLY B 125 " ideal model delta harmonic sigma weight residual 180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N GLY A 125 " pdb=" CA GLY A 125 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS A1195 " pdb=" SG CYS A1195 " pdb=" SG CYS A1212 " pdb=" CB CYS A1212 " ideal model delta sinusoidal sigma weight residual -86.00 -121.63 35.63 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 11052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1537 0.033 - 0.067: 809 0.067 - 0.100: 271 0.100 - 0.134: 109 0.134 - 0.167: 11 Chirality restraints: 2737 Sorted by residual: chirality pdb=" CA VAL A 239 " pdb=" N VAL A 239 " pdb=" C VAL A 239 " pdb=" CB VAL A 239 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL B 239 " pdb=" N VAL B 239 " pdb=" C VAL B 239 " pdb=" CB VAL B 239 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA THR B 818 " pdb=" N THR B 818 " pdb=" C THR B 818 " pdb=" CB THR B 818 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2734 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 755 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 756 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 755 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 756 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 756 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 756 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B1087 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C MET B1087 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B1087 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN B1088 " -0.010 2.00e-02 2.50e+03 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 166 2.42 - 3.04: 11642 3.04 - 3.66: 29651 3.66 - 4.28: 47317 4.28 - 4.90: 76507 Nonbonded interactions: 165283 Sorted by model distance: nonbonded pdb=" O2B TPP B1304 " pdb="MG MG B1306 " model vdw 1.802 2.170 nonbonded pdb=" O2B TPP A1304 " pdb="MG MG A1306 " model vdw 1.807 2.170 nonbonded pdb=" OD2 ASP B 963 " pdb=" O VAL B 993 " model vdw 1.893 3.040 nonbonded pdb=" OD2 ASP A 963 " pdb=" O VAL A 993 " model vdw 1.896 3.040 nonbonded pdb=" O VAL B 993 " pdb="MG MG B1306 " model vdw 1.931 2.170 ... (remaining 165278 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 2 through 691 or resid 693 through 1211 or resid 1213 thro \ ugh 1230 or resid 1301 through 1306)) selection = (chain 'B' and (resid 2 through 691 or resid 693 through 1211 or resid 1213 thro \ ugh 1230 or resid 1301 through 1306)) } 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=0.01 max=1.00 mean=0.99 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.290 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 62.680 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.006 0.048 18506 Z= 0.383 Angle : 0.695 7.323 25055 Z= 0.385 Chirality : 0.046 0.167 2737 Planarity : 0.006 0.052 3245 Dihedral : 14.550 89.678 6743 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.98 % Allowed : 10.60 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.88 (0.17), residues: 2325 helix: 0.06 (0.15), residues: 1048 sheet: -0.62 (0.25), residues: 374 loop : -1.20 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 844 HIS 0.006 0.002 HIS A 214 PHE 0.017 0.002 PHE B 697 TYR 0.017 0.003 TYR A 820 ARG 0.004 0.001 ARG B1027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 305 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.5870 (mtmt) cc_final: 0.5658 (mttt) REVERT: A 36 MET cc_start: 0.8143 (mtm) cc_final: 0.7820 (mtm) REVERT: A 211 GLU cc_start: 0.7265 (mp0) cc_final: 0.6989 (mp0) REVERT: A 253 LEU cc_start: 0.7659 (mp) cc_final: 0.7391 (mp) REVERT: A 328 ASP cc_start: 0.7711 (m-30) cc_final: 0.7465 (m-30) REVERT: A 332 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: A 604 ASP cc_start: 0.5661 (m-30) cc_final: 0.5457 (m-30) REVERT: A 640 LYS cc_start: 0.6675 (tmtt) cc_final: 0.6439 (tmtm) REVERT: A 770 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: A 771 ARG cc_start: 0.7008 (ptm160) cc_final: 0.6235 (ptm-80) REVERT: A 942 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6704 (mp) REVERT: A 1165 HIS cc_start: 0.4451 (t70) cc_final: 0.3686 (t-170) REVERT: A 1197 ARG cc_start: 0.5618 (mmt-90) cc_final: 0.5337 (mmt180) REVERT: B 3 LYS cc_start: 0.5875 (mtmt) cc_final: 0.5662 (mttt) REVERT: B 36 MET cc_start: 0.8186 (mtm) cc_final: 0.7879 (mtm) REVERT: B 211 GLU cc_start: 0.7233 (mp0) cc_final: 0.6880 (mp0) REVERT: B 328 ASP cc_start: 0.7770 (m-30) cc_final: 0.7543 (m-30) REVERT: B 770 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: B 771 ARG cc_start: 0.7002 (ptm160) cc_final: 0.6242 (ptm-80) REVERT: B 942 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6763 (mp) REVERT: B 971 TYR cc_start: 0.7449 (t80) cc_final: 0.6982 (t80) REVERT: B 1132 ASN cc_start: 0.7620 (t0) cc_final: 0.7313 (t0) REVERT: B 1165 HIS cc_start: 0.4805 (t70) cc_final: 0.4158 (t70) REVERT: B 1197 ARG cc_start: 0.5676 (mmt-90) cc_final: 0.5411 (mmt180) outliers start: 93 outliers final: 42 residues processed: 383 average time/residue: 1.2310 time to fit residues: 532.2684 Evaluate side-chains 300 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 770 GLN Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1212 CYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 770 GLN A 836 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN B 836 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18506 Z= 0.167 Angle : 0.509 7.018 25055 Z= 0.268 Chirality : 0.040 0.148 2737 Planarity : 0.004 0.047 3245 Dihedral : 7.232 76.466 2600 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.44 % Allowed : 15.90 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.28 (0.17), residues: 2325 helix: 0.62 (0.16), residues: 1046 sheet: -0.46 (0.26), residues: 374 loop : -0.90 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 844 HIS 0.005 0.001 HIS A 150 PHE 0.015 0.001 PHE A 124 TYR 0.013 0.001 TYR B 967 ARG 0.005 0.000 ARG B 783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 279 time to evaluate : 1.971 Fit side-chains REVERT: A 36 MET cc_start: 0.8125 (mtm) cc_final: 0.7847 (mtm) REVERT: A 135 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: A 211 GLU cc_start: 0.7190 (mp0) cc_final: 0.6776 (mp0) REVERT: A 328 ASP cc_start: 0.7754 (m-30) cc_final: 0.7437 (m-30) REVERT: A 502 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5194 (pm20) REVERT: A 560 ASN cc_start: 0.5706 (OUTLIER) cc_final: 0.5451 (m-40) REVERT: A 604 ASP cc_start: 0.5497 (m-30) cc_final: 0.5272 (m-30) REVERT: A 640 LYS cc_start: 0.6578 (tmtt) cc_final: 0.6343 (tmtm) REVERT: A 704 ILE cc_start: 0.7303 (mp) cc_final: 0.7058 (mm) REVERT: A 771 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6232 (ptm-80) REVERT: A 1132 ASN cc_start: 0.7576 (t0) cc_final: 0.6698 (t0) REVERT: A 1151 GLN cc_start: 0.4894 (mm-40) cc_final: 0.4555 (mm110) REVERT: A 1165 HIS cc_start: 0.4625 (t70) cc_final: 0.3873 (t-170) REVERT: B 36 MET cc_start: 0.8147 (mtm) cc_final: 0.7873 (mtm) REVERT: B 211 GLU cc_start: 0.7273 (mp0) cc_final: 0.6887 (mp0) REVERT: B 328 ASP cc_start: 0.7819 (m-30) cc_final: 0.7516 (m-30) REVERT: B 604 ASP cc_start: 0.5616 (m-30) cc_final: 0.5351 (m-30) REVERT: B 704 ILE cc_start: 0.7343 (mp) cc_final: 0.7088 (mm) REVERT: B 771 ARG cc_start: 0.6956 (ptm160) cc_final: 0.6274 (ptm-80) REVERT: B 971 TYR cc_start: 0.7407 (t80) cc_final: 0.6977 (t80) REVERT: B 1132 ASN cc_start: 0.7527 (t0) cc_final: 0.6629 (t0) REVERT: B 1151 GLN cc_start: 0.4887 (mm-40) cc_final: 0.4585 (mm110) REVERT: B 1165 HIS cc_start: 0.4670 (t70) cc_final: 0.3961 (t-170) REVERT: B 1197 ARG cc_start: 0.5598 (mmt-90) cc_final: 0.5318 (mmt180) outliers start: 64 outliers final: 26 residues processed: 320 average time/residue: 1.2000 time to fit residues: 435.6304 Evaluate side-chains 275 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18506 Z= 0.283 Angle : 0.584 6.959 25055 Z= 0.308 Chirality : 0.043 0.160 2737 Planarity : 0.005 0.049 3245 Dihedral : 6.346 56.963 2560 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.55 % Allowed : 18.60 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.46 (0.17), residues: 2325 helix: 0.46 (0.16), residues: 1046 sheet: -0.50 (0.26), residues: 374 loop : -1.00 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 844 HIS 0.005 0.001 HIS B 976 PHE 0.020 0.002 PHE B 124 TYR 0.013 0.002 TYR B 820 ARG 0.004 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.7085 (mmm) REVERT: A 36 MET cc_start: 0.8147 (mtm) cc_final: 0.7807 (mtm) REVERT: A 197 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: A 202 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 211 GLU cc_start: 0.7196 (mp0) cc_final: 0.6843 (mp0) REVERT: A 328 ASP cc_start: 0.7692 (m-30) cc_final: 0.7382 (m-30) REVERT: A 561 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5799 (mpt) REVERT: A 604 ASP cc_start: 0.5553 (m-30) cc_final: 0.5277 (m-30) REVERT: A 613 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4994 (mt) REVERT: A 640 LYS cc_start: 0.6618 (tmtt) cc_final: 0.6409 (tmtm) REVERT: A 704 ILE cc_start: 0.7167 (mp) cc_final: 0.6864 (mm) REVERT: A 771 ARG cc_start: 0.6866 (ptm160) cc_final: 0.6234 (ptm-80) REVERT: A 942 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6683 (mp) REVERT: A 1132 ASN cc_start: 0.7623 (t0) cc_final: 0.6690 (t0) REVERT: A 1165 HIS cc_start: 0.4545 (t70) cc_final: 0.3835 (t-170) REVERT: B 5 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7195 (mmm) REVERT: B 36 MET cc_start: 0.8192 (mtm) cc_final: 0.7862 (mtm) REVERT: B 202 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: B 211 GLU cc_start: 0.7299 (mp0) cc_final: 0.6926 (mp0) REVERT: B 328 ASP cc_start: 0.7741 (m-30) cc_final: 0.7436 (m-30) REVERT: B 502 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5221 (pm20) REVERT: B 561 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5717 (mpt) REVERT: B 613 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.5168 (mt) REVERT: B 704 ILE cc_start: 0.7228 (mp) cc_final: 0.6906 (mm) REVERT: B 771 ARG cc_start: 0.6975 (ptm160) cc_final: 0.6303 (ptm-80) REVERT: B 942 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6638 (mp) REVERT: B 971 TYR cc_start: 0.7470 (t80) cc_final: 0.7166 (t80) REVERT: B 1132 ASN cc_start: 0.7592 (t0) cc_final: 0.6625 (t0) REVERT: B 1165 HIS cc_start: 0.4666 (t70) cc_final: 0.4063 (t70) REVERT: B 1197 ARG cc_start: 0.5659 (mmt-90) cc_final: 0.5448 (mmt180) outliers start: 66 outliers final: 32 residues processed: 280 average time/residue: 1.3106 time to fit residues: 412.9850 Evaluate side-chains 279 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18506 Z= 0.200 Angle : 0.527 6.917 25055 Z= 0.277 Chirality : 0.041 0.150 2737 Planarity : 0.004 0.046 3245 Dihedral : 5.975 58.222 2552 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.44 % Allowed : 19.34 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.31 (0.17), residues: 2325 helix: 0.64 (0.16), residues: 1042 sheet: -0.44 (0.26), residues: 364 loop : -0.99 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 844 HIS 0.004 0.001 HIS A 150 PHE 0.024 0.002 PHE A1099 TYR 0.010 0.001 TYR A 820 ARG 0.004 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 246 time to evaluate : 1.974 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8113 (mtm) cc_final: 0.7817 (mtm) REVERT: A 197 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: A 202 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: A 211 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: A 328 ASP cc_start: 0.7715 (m-30) cc_final: 0.7383 (m-30) REVERT: A 502 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5144 (pm20) REVERT: A 561 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.5794 (mpt) REVERT: A 604 ASP cc_start: 0.5486 (m-30) cc_final: 0.5213 (m-30) REVERT: A 640 LYS cc_start: 0.6619 (tmtt) cc_final: 0.6404 (tmtm) REVERT: A 704 ILE cc_start: 0.7310 (mp) cc_final: 0.7085 (mm) REVERT: A 737 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7128 (ttt-90) REVERT: A 771 ARG cc_start: 0.6881 (ptm160) cc_final: 0.6275 (ptm-80) REVERT: A 942 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6580 (mp) REVERT: A 1132 ASN cc_start: 0.7539 (t0) cc_final: 0.6648 (t0) REVERT: A 1165 HIS cc_start: 0.4600 (t70) cc_final: 0.3854 (t-170) REVERT: B 5 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7158 (mmm) REVERT: B 36 MET cc_start: 0.8156 (mtm) cc_final: 0.7866 (mtm) REVERT: B 202 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: B 211 GLU cc_start: 0.7293 (mp0) cc_final: 0.6899 (mp0) REVERT: B 328 ASP cc_start: 0.7759 (m-30) cc_final: 0.7427 (m-30) REVERT: B 485 ASP cc_start: 0.6925 (m-30) cc_final: 0.6284 (t0) REVERT: B 704 ILE cc_start: 0.7189 (mp) cc_final: 0.6948 (mm) REVERT: B 737 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7170 (ttt-90) REVERT: B 771 ARG cc_start: 0.6902 (ptm160) cc_final: 0.6268 (ptm-80) REVERT: B 942 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6639 (mp) REVERT: B 971 TYR cc_start: 0.7463 (t80) cc_final: 0.6826 (t80) REVERT: B 1132 ASN cc_start: 0.7536 (t0) cc_final: 0.6616 (t0) REVERT: B 1165 HIS cc_start: 0.4656 (t70) cc_final: 0.4024 (t-170) outliers start: 64 outliers final: 35 residues processed: 288 average time/residue: 1.3320 time to fit residues: 430.7155 Evaluate side-chains 284 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18506 Z= 0.310 Angle : 0.608 7.443 25055 Z= 0.320 Chirality : 0.044 0.160 2737 Planarity : 0.005 0.050 3245 Dihedral : 6.230 57.570 2550 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.66 % Allowed : 19.29 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.57 (0.17), residues: 2325 helix: 0.36 (0.16), residues: 1042 sheet: -0.53 (0.25), residues: 376 loop : -1.06 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 844 HIS 0.005 0.001 HIS B 976 PHE 0.029 0.002 PHE A1099 TYR 0.034 0.002 TYR A 971 ARG 0.004 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 242 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8140 (mtm) cc_final: 0.7766 (mtm) REVERT: A 197 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: A 211 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: A 328 ASP cc_start: 0.7698 (m-30) cc_final: 0.7392 (m-30) REVERT: A 502 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.5053 (pm20) REVERT: A 519 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 561 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5818 (mpt) REVERT: A 604 ASP cc_start: 0.5525 (m-30) cc_final: 0.5257 (m-30) REVERT: A 613 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4877 (mt) REVERT: A 640 LYS cc_start: 0.6574 (tmtt) cc_final: 0.6365 (tmtm) REVERT: A 704 ILE cc_start: 0.7277 (mp) cc_final: 0.6953 (mm) REVERT: A 771 ARG cc_start: 0.6892 (ptm160) cc_final: 0.6276 (ptm-80) REVERT: A 921 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5401 (tt) REVERT: A 942 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6680 (mp) REVERT: A 1132 ASN cc_start: 0.7551 (t0) cc_final: 0.7216 (t0) REVERT: A 1165 HIS cc_start: 0.4607 (t70) cc_final: 0.3994 (t-170) REVERT: B 5 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7148 (mmm) REVERT: B 36 MET cc_start: 0.8184 (mtm) cc_final: 0.7823 (mtm) REVERT: B 211 GLU cc_start: 0.7274 (mp0) cc_final: 0.6839 (mp0) REVERT: B 328 ASP cc_start: 0.7791 (m-30) cc_final: 0.7480 (m-30) REVERT: B 561 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5828 (mpt) REVERT: B 613 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5211 (mt) REVERT: B 704 ILE cc_start: 0.7192 (mp) cc_final: 0.6829 (mm) REVERT: B 771 ARG cc_start: 0.6944 (ptm160) cc_final: 0.6307 (ptm-80) REVERT: B 942 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6635 (mp) REVERT: B 971 TYR cc_start: 0.7537 (t80) cc_final: 0.7156 (t80) REVERT: B 1132 ASN cc_start: 0.7584 (t0) cc_final: 0.6697 (t0) REVERT: B 1165 HIS cc_start: 0.4785 (t70) cc_final: 0.4226 (t70) outliers start: 87 outliers final: 40 residues processed: 300 average time/residue: 1.3343 time to fit residues: 449.0667 Evaluate side-chains 294 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1151 GLN Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 0.0040 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18506 Z= 0.267 Angle : 0.580 7.604 25055 Z= 0.305 Chirality : 0.043 0.155 2737 Planarity : 0.005 0.049 3245 Dihedral : 6.093 58.753 2548 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.87 % Allowed : 20.30 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.55 (0.17), residues: 2325 helix: 0.42 (0.16), residues: 1042 sheet: -0.54 (0.26), residues: 364 loop : -1.09 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 844 HIS 0.004 0.001 HIS B 976 PHE 0.026 0.002 PHE A1099 TYR 0.019 0.002 TYR A 971 ARG 0.004 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 247 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8141 (mtm) cc_final: 0.7789 (mtm) REVERT: A 197 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: A 202 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: A 211 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: A 328 ASP cc_start: 0.7712 (m-30) cc_final: 0.7395 (m-30) REVERT: A 561 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5831 (mpt) REVERT: A 604 ASP cc_start: 0.5523 (m-30) cc_final: 0.5256 (m-30) REVERT: A 613 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4833 (mt) REVERT: A 640 LYS cc_start: 0.6611 (tmtt) cc_final: 0.6387 (tmtm) REVERT: A 704 ILE cc_start: 0.7250 (mp) cc_final: 0.6945 (mm) REVERT: A 771 ARG cc_start: 0.6877 (ptm160) cc_final: 0.5938 (ptp90) REVERT: A 803 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6143 (tt0) REVERT: A 921 ILE cc_start: 0.5786 (OUTLIER) cc_final: 0.5328 (tt) REVERT: A 942 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6665 (mp) REVERT: A 1132 ASN cc_start: 0.7511 (t0) cc_final: 0.7203 (t0) REVERT: A 1165 HIS cc_start: 0.4616 (t70) cc_final: 0.4008 (t-170) REVERT: B 5 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7166 (mmm) REVERT: B 36 MET cc_start: 0.8183 (mtm) cc_final: 0.7848 (mtm) REVERT: B 202 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: B 211 GLU cc_start: 0.7240 (mp0) cc_final: 0.6845 (mp0) REVERT: B 328 ASP cc_start: 0.7799 (m-30) cc_final: 0.7479 (m-30) REVERT: B 561 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5828 (mpt) REVERT: B 613 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5180 (mt) REVERT: B 704 ILE cc_start: 0.7162 (mp) cc_final: 0.6802 (mm) REVERT: B 771 ARG cc_start: 0.6930 (ptm160) cc_final: 0.6312 (ptm-80) REVERT: B 942 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6616 (mp) REVERT: B 971 TYR cc_start: 0.7529 (t80) cc_final: 0.7276 (t80) REVERT: B 1132 ASN cc_start: 0.7552 (t0) cc_final: 0.6725 (t0) REVERT: B 1165 HIS cc_start: 0.4715 (t70) cc_final: 0.4134 (t-170) outliers start: 72 outliers final: 34 residues processed: 293 average time/residue: 1.3333 time to fit residues: 438.2984 Evaluate side-chains 285 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18506 Z= 0.169 Angle : 0.521 9.022 25055 Z= 0.271 Chirality : 0.040 0.144 2737 Planarity : 0.004 0.045 3245 Dihedral : 5.718 59.459 2546 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.97 % Allowed : 21.30 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.24 (0.17), residues: 2325 helix: 0.71 (0.16), residues: 1040 sheet: -0.46 (0.26), residues: 364 loop : -0.96 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 844 HIS 0.005 0.001 HIS A 150 PHE 0.019 0.001 PHE A 124 TYR 0.013 0.001 TYR A 971 ARG 0.004 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8096 (mtm) cc_final: 0.7824 (mtm) REVERT: A 202 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: A 211 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: A 328 ASP cc_start: 0.7722 (m-30) cc_final: 0.7390 (m-30) REVERT: A 413 THR cc_start: 0.6851 (m) cc_final: 0.6245 (p) REVERT: A 485 ASP cc_start: 0.6962 (m-30) cc_final: 0.6369 (t0) REVERT: A 560 ASN cc_start: 0.5533 (OUTLIER) cc_final: 0.3739 (t0) REVERT: A 604 ASP cc_start: 0.5450 (m-30) cc_final: 0.5178 (m-30) REVERT: A 640 LYS cc_start: 0.6567 (tmtt) cc_final: 0.6345 (tmtm) REVERT: A 771 ARG cc_start: 0.6867 (ptm160) cc_final: 0.5970 (ptp90) REVERT: A 803 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: A 831 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7419 (ppt-90) REVERT: A 1132 ASN cc_start: 0.7511 (t0) cc_final: 0.6593 (t0) REVERT: B 36 MET cc_start: 0.8139 (mtm) cc_final: 0.7867 (mtm) REVERT: B 211 GLU cc_start: 0.7329 (mp0) cc_final: 0.6952 (mp0) REVERT: B 328 ASP cc_start: 0.7794 (m-30) cc_final: 0.7449 (m-30) REVERT: B 413 THR cc_start: 0.7016 (m) cc_final: 0.6359 (p) REVERT: B 485 ASP cc_start: 0.6885 (m-30) cc_final: 0.6340 (t0) REVERT: B 771 ARG cc_start: 0.6904 (ptm160) cc_final: 0.6047 (ptp90) REVERT: B 831 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7430 (ppt-90) REVERT: B 971 TYR cc_start: 0.7537 (t80) cc_final: 0.7328 (t80) REVERT: B 1132 ASN cc_start: 0.7543 (t0) cc_final: 0.6671 (t0) outliers start: 55 outliers final: 27 residues processed: 293 average time/residue: 1.2544 time to fit residues: 414.3897 Evaluate side-chains 286 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18506 Z= 0.234 Angle : 0.568 11.102 25055 Z= 0.296 Chirality : 0.042 0.158 2737 Planarity : 0.004 0.047 3245 Dihedral : 5.835 58.699 2546 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.38 % Allowed : 22.36 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2325 helix: 0.61 (0.16), residues: 1040 sheet: -0.47 (0.26), residues: 364 loop : -0.98 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 844 HIS 0.004 0.001 HIS B 150 PHE 0.022 0.002 PHE B 124 TYR 0.016 0.002 TYR A 971 ARG 0.003 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.150 Fit side-chains REVERT: A 36 MET cc_start: 0.8123 (mtm) cc_final: 0.7819 (mtm) REVERT: A 202 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: A 211 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: A 276 MET cc_start: 0.8430 (ttp) cc_final: 0.8216 (ptm) REVERT: A 328 ASP cc_start: 0.7696 (m-30) cc_final: 0.7370 (m-30) REVERT: A 413 THR cc_start: 0.6855 (m) cc_final: 0.6161 (p) REVERT: A 485 ASP cc_start: 0.6981 (m-30) cc_final: 0.6364 (t0) REVERT: A 604 ASP cc_start: 0.5409 (m-30) cc_final: 0.5135 (m-30) REVERT: A 640 LYS cc_start: 0.6573 (tmtt) cc_final: 0.6355 (tmtm) REVERT: A 771 ARG cc_start: 0.6854 (ptm160) cc_final: 0.5960 (ptp90) REVERT: A 1132 ASN cc_start: 0.7579 (t0) cc_final: 0.7269 (t0) REVERT: B 36 MET cc_start: 0.8156 (mtm) cc_final: 0.7861 (mtm) REVERT: B 211 GLU cc_start: 0.7353 (mp0) cc_final: 0.6956 (mp0) REVERT: B 328 ASP cc_start: 0.7769 (m-30) cc_final: 0.7438 (m-30) REVERT: B 485 ASP cc_start: 0.6855 (m-30) cc_final: 0.6298 (t0) REVERT: B 771 ARG cc_start: 0.6904 (ptm160) cc_final: 0.6045 (ptp90) REVERT: B 831 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7462 (ppt-90) REVERT: B 971 TYR cc_start: 0.7526 (t80) cc_final: 0.7244 (t80) REVERT: B 1027 ARG cc_start: 0.5887 (mtp180) cc_final: 0.5164 (ttp-110) REVERT: B 1132 ASN cc_start: 0.7557 (t0) cc_final: 0.6694 (t0) outliers start: 44 outliers final: 31 residues processed: 280 average time/residue: 1.2927 time to fit residues: 407.3936 Evaluate side-chains 277 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 128 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18506 Z= 0.181 Angle : 0.538 11.702 25055 Z= 0.279 Chirality : 0.041 0.151 2737 Planarity : 0.004 0.045 3245 Dihedral : 5.673 58.620 2546 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 22.73 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.19 (0.17), residues: 2325 helix: 0.72 (0.16), residues: 1040 sheet: -0.41 (0.26), residues: 364 loop : -0.88 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 844 HIS 0.005 0.001 HIS A 150 PHE 0.021 0.001 PHE B 124 TYR 0.030 0.001 TYR A 971 ARG 0.004 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8106 (mtm) cc_final: 0.7819 (mtm) REVERT: A 211 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: A 328 ASP cc_start: 0.7725 (m-30) cc_final: 0.7393 (m-30) REVERT: A 413 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6175 (p) REVERT: A 485 ASP cc_start: 0.6955 (m-30) cc_final: 0.6377 (t0) REVERT: A 560 ASN cc_start: 0.5542 (OUTLIER) cc_final: 0.3763 (t0) REVERT: A 604 ASP cc_start: 0.5456 (m-30) cc_final: 0.5182 (m-30) REVERT: A 640 LYS cc_start: 0.6552 (tmtt) cc_final: 0.6336 (tmtm) REVERT: A 771 ARG cc_start: 0.6868 (ptm160) cc_final: 0.5983 (ptp90) REVERT: A 1132 ASN cc_start: 0.7534 (t0) cc_final: 0.7209 (t0) REVERT: B 36 MET cc_start: 0.8136 (mtm) cc_final: 0.7865 (mtm) REVERT: B 197 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: B 211 GLU cc_start: 0.7357 (mp0) cc_final: 0.6963 (mp0) REVERT: B 328 ASP cc_start: 0.7808 (m-30) cc_final: 0.7447 (m-30) REVERT: B 485 ASP cc_start: 0.6786 (m-30) cc_final: 0.6259 (t0) REVERT: B 771 ARG cc_start: 0.6887 (ptm160) cc_final: 0.6042 (ptp90) REVERT: B 921 ILE cc_start: 0.5792 (OUTLIER) cc_final: 0.5331 (mp) REVERT: B 971 TYR cc_start: 0.7517 (t80) cc_final: 0.7306 (t80) REVERT: B 1132 ASN cc_start: 0.7541 (t0) cc_final: 0.6688 (t0) outliers start: 44 outliers final: 25 residues processed: 278 average time/residue: 1.3118 time to fit residues: 411.0897 Evaluate side-chains 275 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1151 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 0.0030 chunk 214 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN A 128 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 18506 Z= 0.203 Angle : 0.728 59.164 25055 Z= 0.410 Chirality : 0.041 0.150 2737 Planarity : 0.004 0.045 3245 Dihedral : 5.510 58.579 2533 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.91 % Allowed : 23.05 % Favored : 75.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.56 % 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: -0.19 (0.17), residues: 2325 helix: 0.71 (0.16), residues: 1040 sheet: -0.40 (0.26), residues: 364 loop : -0.88 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 844 HIS 0.005 0.001 HIS A 150 PHE 0.019 0.001 PHE B 124 TYR 0.026 0.001 TYR A 971 ARG 0.008 0.000 ARG A 831 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 2.043 Fit side-chains REVERT: A 36 MET cc_start: 0.8105 (mtm) cc_final: 0.7820 (mtm) REVERT: A 211 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: A 328 ASP cc_start: 0.7735 (m-30) cc_final: 0.7393 (m-30) REVERT: A 413 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6173 (p) REVERT: A 485 ASP cc_start: 0.6960 (m-30) cc_final: 0.6380 (t0) REVERT: A 560 ASN cc_start: 0.5547 (OUTLIER) cc_final: 0.3766 (t0) REVERT: A 604 ASP cc_start: 0.5460 (m-30) cc_final: 0.5182 (m-30) REVERT: A 640 LYS cc_start: 0.6556 (tmtt) cc_final: 0.6337 (tmtm) REVERT: A 771 ARG cc_start: 0.6868 (ptm160) cc_final: 0.5984 (ptp90) REVERT: A 1132 ASN cc_start: 0.7532 (t0) cc_final: 0.7209 (t0) REVERT: B 36 MET cc_start: 0.8137 (mtm) cc_final: 0.7864 (mtm) REVERT: B 197 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: B 211 GLU cc_start: 0.7337 (mp0) cc_final: 0.6963 (mp0) REVERT: B 328 ASP cc_start: 0.7804 (m-30) cc_final: 0.7446 (m-30) REVERT: B 485 ASP cc_start: 0.6787 (m-30) cc_final: 0.6260 (t0) REVERT: B 771 ARG cc_start: 0.6887 (ptm160) cc_final: 0.6041 (ptp90) REVERT: B 921 ILE cc_start: 0.5777 (OUTLIER) cc_final: 0.5329 (mp) REVERT: B 971 TYR cc_start: 0.7514 (t80) cc_final: 0.7305 (t80) REVERT: B 1132 ASN cc_start: 0.7541 (t0) cc_final: 0.6690 (t0) outliers start: 35 outliers final: 25 residues processed: 269 average time/residue: 1.2999 time to fit residues: 394.2141 Evaluate side-chains 275 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.185154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162366 restraints weight = 35871.266| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.02 r_work: 0.3565 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 110 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 18506 Z= 0.203 Angle : 0.728 59.164 25055 Z= 0.410 Chirality : 0.041 0.150 2737 Planarity : 0.004 0.045 3245 Dihedral : 5.510 58.579 2533 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 23.21 % Favored : 75.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.56 % 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: -0.19 (0.17), residues: 2325 helix: 0.71 (0.16), residues: 1040 sheet: -0.40 (0.26), residues: 364 loop : -0.88 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 844 HIS 0.005 0.001 HIS A 150 PHE 0.019 0.001 PHE B 124 TYR 0.026 0.001 TYR A 971 ARG 0.008 0.000 ARG A 831 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6843.55 seconds wall clock time: 122 minutes 35.95 seconds (7355.95 seconds total)