Starting phenix.real_space_refine on Sun Mar 24 04:35:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/03_2024/8e6z_27931_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Zn 2 6.06 5 P 97 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17415 2.51 5 N 4980 2.21 5 O 5658 1.98 5 H 11239 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ASP 912": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 86": "OE1" <-> "OE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39505 Number of models: 1 Model: "" Number of chains: 10 Chain: "5" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 913 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "6" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1029 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 676 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 5, 'rna3p': 21} Chain: "A" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "B" Number of atoms: 21000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 21000 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "C" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 550 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1392 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14070 SG CYS B 70 106.877 63.429 62.635 1.00 45.60 S ATOM 14329 SG CYS B 85 111.495 64.726 62.469 1.00 49.94 S ATOM 25911 SG CYS B 814 77.254 78.320 122.735 1.00 22.38 S ATOM 27048 SG CYS B 888 76.943 78.146 118.214 1.00 20.48 S ATOM 27139 SG CYS B 895 76.573 75.353 120.516 1.00 14.28 S ATOM 27176 SG CYS B 898 74.004 77.643 121.396 1.00 16.02 S Time building chain proxies: 19.66, per 1000 atoms: 0.50 Number of scatterers: 39505 At special positions: 0 Unit cell: (166.764, 162.488, 160.35, 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) Zn 2 29.99 S 113 16.00 P 97 15.00 Mg 1 11.99 O 5658 8.00 N 4980 7.00 C 17415 6.00 H 11239 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 88 " distance=2.12 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 Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Atom "ATOM 311 O5' DA 5 100 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.57 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1502 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 70 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 85 " pdb=" ZN B1503 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 888 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 895 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 814 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 898 " Number of angles added : 6 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6194 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 35.6% alpha, 15.0% beta 28 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 13.77 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 48 through 56 removed outlier: 4.129A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.840A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 167 " --> pdb=" O THR A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.057A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.579A pdb=" N ARG A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.688A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 4.129A pdb=" N PHE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.758A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.512A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 609 through 614 removed outlier: 4.046A pdb=" N ASN A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 614' Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 738 through 741 removed outlier: 3.792A pdb=" N MET A 741 " --> pdb=" O GLU A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.932A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 981 removed outlier: 4.146A pdb=" N ALA A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 998 removed outlier: 3.589A pdb=" N LEU A 998 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1038 removed outlier: 3.627A pdb=" N GLN A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.548A pdb=" N SER A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1106' Processing helix chain 'A' and resid 1109 through 1134 removed outlier: 3.695A pdb=" N LEU A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.879A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 4.191A pdb=" N THR A1163 " --> pdb=" O ASP A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1177 Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.552A pdb=" N GLY A1202 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1281 removed outlier: 3.625A pdb=" N TYR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1297 through 1310 Processing helix chain 'A' and resid 1320 through 1332 removed outlier: 3.651A pdb=" N ASN A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.745A pdb=" N ALA B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.777A pdb=" N ARG B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.808A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 removed outlier: 3.904A pdb=" N ASN B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.547A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.689A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.566A pdb=" N ILE B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.649A pdb=" N CYS B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.521A pdb=" N LEU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.610A pdb=" N ALA B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.645A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.533A pdb=" N SER B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 703 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.861A pdb=" N ILE B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 805 removed outlier: 3.851A pdb=" N GLY B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 805 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.642A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.797A pdb=" N ASN B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.522A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 914 through 925 removed outlier: 4.007A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 1137 through 1146 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 4.195A pdb=" N VAL B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1250 through 1261 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.542A pdb=" N ALA B1294 " --> pdb=" O ARG B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1315 Processing helix chain 'B' and resid 1327 through 1339 removed outlier: 3.828A pdb=" N VAL B1331 " --> pdb=" O GLU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1346 through 1353 removed outlier: 3.806A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.419A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.548A pdb=" N THR C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.840A pdb=" N VAL C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'D' and resid 34 through 50 removed outlier: 4.040A pdb=" N THR D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.560A pdb=" N GLY D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 212 through 227 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.527A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 71 Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 39 removed outlier: 3.816A pdb=" N PHE F 39 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.570A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.927A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 73 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 97 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 75 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 94 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 96 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.321A pdb=" N SER A 147 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.580A pdb=" N LEU A 184 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.576A pdb=" N ALA A 257 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.193A pdb=" N TYR A 301 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 593 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 602 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.632A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 733 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 758 removed outlier: 3.995A pdb=" N THR A 757 " --> pdb=" O ILE A 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.590A pdb=" N ASP A 790 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.452A pdb=" N THR A1226 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 816 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A1079 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 818 " --> pdb=" O ILE A1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1066 through 1067 Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.412A pdb=" N ASP A 842 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1046 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 882 through 884 removed outlier: 3.626A pdb=" N VAL A 884 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AC3, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC4, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC5, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC6, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.452A pdb=" N SER B 34 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS B 104 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 106 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 107 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.414A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.685A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD3, first strand: chain 'B' and resid 849 through 850 removed outlier: 4.608A pdb=" N ASP B 855 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.803A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD6, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.619A pdb=" N ARG B1036 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.089A pdb=" N GLN B1049 " --> pdb=" O SER B1058 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B1058 " --> pdb=" O GLN B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD9, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.340A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.521A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.248A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE C 61 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 143 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE5, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 23 through 31 removed outlier: 7.013A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.075A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE9, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.050A pdb=" N CYS D 131 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.624A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 68 through 73 removed outlier: 7.688A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.685A pdb=" N GLU F 149 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 17.91 Time building geometry restraints manager: 25.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11195 1.03 - 1.23: 464 1.23 - 1.42: 11396 1.42 - 1.62: 16870 1.62 - 1.82: 203 Bond restraints: 40128 Sorted by residual: bond pdb=" C PHE A 828 " pdb=" N THR A 829 " ideal model delta sigma weight residual 1.331 1.535 -0.205 1.43e-02 4.89e+03 2.05e+02 bond pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.36e-02 5.41e+03 1.95e+02 bond pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 1.523 1.687 -0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" N3 U 7 17 " pdb=" H3 U 7 17 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N3 DT 6 24 " pdb=" H3 DT 6 24 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 40123 not shown) Histogram of bond angle deviations from ideal: 59.62 - 77.29: 2 77.29 - 94.97: 2 94.97 - 112.64: 36530 112.64 - 130.31: 28414 130.31 - 147.99: 126 Bond angle restraints: 65074 Sorted by residual: angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" O5' DA 6 28 " ideal model delta sigma weight residual 104.00 147.99 -43.99 1.50e+00 4.44e-01 8.60e+02 angle pdb=" H2' DA 5 110 " pdb=" C2' DA 5 110 " pdb="H2'' DA 5 110 " ideal model delta sigma weight residual 109.00 75.98 33.02 1.50e+00 4.44e-01 4.85e+02 angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" OP1 DA 6 28 " ideal model delta sigma weight residual 108.00 59.62 48.38 3.00e+00 1.11e-01 2.60e+02 angle pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.07 -22.07 1.50e+00 4.44e-01 2.16e+02 angle pdb=" CA PRO F 102 " pdb=" C PRO F 102 " pdb=" N ILE F 103 " ideal model delta sigma weight residual 115.12 131.74 -16.62 1.25e+00 6.40e-01 1.77e+02 ... (remaining 65069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20084 35.99 - 71.98: 876 71.98 - 107.97: 28 107.97 - 143.96: 2 143.96 - 179.95: 9 Dihedral angle restraints: 20999 sinusoidal: 10953 harmonic: 10046 Sorted by residual: dihedral pdb=" CA VAL C 192 " pdb=" C VAL C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -126.65 -53.35 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 16 " pdb=" C1' U 7 16 " pdb=" N1 U 7 16 " pdb=" C2 U 7 16 " ideal model delta sinusoidal sigma weight residual 200.00 43.62 156.38 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" CA GLN B1326 " pdb=" C GLN B1326 " pdb=" N GLU B1327 " pdb=" CA GLU B1327 " ideal model delta harmonic sigma weight residual -180.00 -138.06 -41.94 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 20996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 4126 0.113 - 0.227: 361 0.227 - 0.340: 19 0.340 - 0.454: 4 0.454 - 0.567: 2 Chirality restraints: 4512 Sorted by residual: chirality pdb=" C3' U 7 17 " pdb=" C4' U 7 17 " pdb=" O3' U 7 17 " pdb=" C2' U 7 17 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CB ILE A1079 " pdb=" CA ILE A1079 " pdb=" CG1 ILE A1079 " pdb=" CG2 ILE A1079 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA TYR B 46 " pdb=" N TYR B 46 " pdb=" C TYR B 46 " pdb=" CB TYR B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4509 not shown) Planarity restraints: 6142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.211 2.00e-02 2.50e+03 2.51e-01 9.44e+02 pdb=" CG ASN B 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " -0.203 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " 0.385 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " -0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 285 " -0.032 2.00e-02 2.50e+03 6.04e-02 3.64e+01 pdb=" N ALA B 286 " 0.104 2.00e-02 2.50e+03 pdb=" CA ALA B 286 " -0.027 2.00e-02 2.50e+03 pdb=" H ALA B 286 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 41 " 0.028 2.00e-02 2.50e+03 6.00e-02 3.59e+01 pdb=" C GLU F 41 " -0.103 2.00e-02 2.50e+03 pdb=" O GLU F 41 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL F 42 " 0.032 2.00e-02 2.50e+03 ... (remaining 6139 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 97 1.75 - 2.46: 15019 2.46 - 3.18: 81511 3.18 - 3.89: 122426 3.89 - 4.60: 189298 Nonbonded interactions: 408351 Sorted by model distance: nonbonded pdb=" C5' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.038 3.100 nonbonded pdb=" O PRO A 847 " pdb=" CB PRO A 889 " model vdw 1.117 3.100 nonbonded pdb=" O5' DA 5 100 " pdb=" CB SER F 16 " model vdw 1.140 3.100 nonbonded pdb=" C4' DA 5 100 " pdb=" OG SER F 16 " model vdw 1.219 3.100 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 32 " model vdw 1.266 2.100 ... (remaining 408346 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 'C' and (resid 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 169 through 232)) selection = (chain 'D' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.720 Extract box with map and model: 14.030 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 130.560 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 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 : 0.010 0.205 28889 Z= 0.630 Angle : 1.193 48.381 39430 Z= 0.689 Chirality : 0.067 0.567 4512 Planarity : 0.008 0.081 4824 Dihedral : 16.108 163.715 11425 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.78 % Favored : 90.59 % Rotamer: Outliers : 4.31 % Allowed : 4.69 % Favored : 91.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.11), residues: 3338 helix: -2.92 (0.11), residues: 1101 sheet: -2.25 (0.24), residues: 409 loop : -3.11 (0.12), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 PHE 0.035 0.003 PHE B 620 TYR 0.038 0.003 TYR A1229 ARG 0.013 0.001 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 542 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.6711 (mt) cc_final: 0.6150 (mt) REVERT: A 469 VAL cc_start: 0.7968 (m) cc_final: 0.6851 (t) REVERT: A 516 ASP cc_start: 0.7051 (p0) cc_final: 0.6712 (p0) REVERT: A 681 MET cc_start: 0.6853 (mtp) cc_final: 0.6222 (mtm) REVERT: A 1308 ILE cc_start: 0.7312 (mm) cc_final: 0.6915 (mm) REVERT: B 70 CYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7335 (t) REVERT: B 119 SER cc_start: 0.6413 (OUTLIER) cc_final: 0.5927 (p) REVERT: B 363 LEU cc_start: 0.7461 (pp) cc_final: 0.6996 (pp) REVERT: F 44 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6817 (t) REVERT: F 123 ARG cc_start: -0.0724 (OUTLIER) cc_final: -0.1179 (mtt180) outliers start: 123 outliers final: 28 residues processed: 643 average time/residue: 0.7100 time to fit residues: 683.7423 Evaluate side-chains 322 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 290 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.2980 chunk 258 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 330 HIS A 437 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 618 GLN A 761 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN B 294 ASN B 606 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28889 Z= 0.187 Angle : 0.585 9.423 39430 Z= 0.318 Chirality : 0.041 0.165 4512 Planarity : 0.005 0.058 4824 Dihedral : 16.799 170.511 4859 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.02 % Favored : 93.77 % Rotamer: Outliers : 0.14 % Allowed : 1.68 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.13), residues: 3338 helix: -0.53 (0.15), residues: 1118 sheet: -2.03 (0.23), residues: 463 loop : -2.56 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.008 0.001 HIS B 777 PHE 0.017 0.001 PHE F 64 TYR 0.019 0.001 TYR F 68 ARG 0.008 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 685 MET cc_start: 0.7252 (mtt) cc_final: 0.6980 (mtm) REVERT: B 147 ILE cc_start: 0.5018 (pt) cc_final: 0.4577 (tp) REVERT: E 49 ILE cc_start: 0.9038 (pt) cc_final: 0.8523 (pt) outliers start: 4 outliers final: 1 residues processed: 336 average time/residue: 0.6350 time to fit residues: 332.0951 Evaluate side-chains 241 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 257 optimal weight: 0.5980 chunk 210 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 248 optimal weight: 0.3980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS A 808 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 651 HIS ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28889 Z= 0.214 Angle : 0.570 13.959 39430 Z= 0.307 Chirality : 0.040 0.161 4512 Planarity : 0.004 0.048 4824 Dihedral : 16.568 170.602 4859 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 29.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3338 helix: 0.72 (0.16), residues: 1119 sheet: -1.63 (0.24), residues: 458 loop : -2.19 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A1276 HIS 0.008 0.001 HIS B 651 PHE 0.022 0.001 PHE A1270 TYR 0.039 0.002 TYR B 631 ARG 0.007 0.001 ARG B1222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 685 MET cc_start: 0.7649 (mtt) cc_final: 0.7352 (mtm) REVERT: A 1325 VAL cc_start: 0.8723 (t) cc_final: 0.8510 (t) REVERT: B 372 MET cc_start: 0.7364 (mmm) cc_final: 0.6149 (mtt) REVERT: B 722 ILE cc_start: 0.8617 (pt) cc_final: 0.8396 (mt) REVERT: B 1257 VAL cc_start: 0.8225 (t) cc_final: 0.7867 (t) outliers start: 1 outliers final: 1 residues processed: 286 average time/residue: 0.6601 time to fit residues: 297.8602 Evaluate side-chains 222 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 28889 Z= 0.325 Angle : 0.660 16.327 39430 Z= 0.350 Chirality : 0.042 0.470 4512 Planarity : 0.005 0.049 4824 Dihedral : 16.618 170.485 4859 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.43 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3338 helix: 0.76 (0.15), residues: 1139 sheet: -1.56 (0.24), residues: 461 loop : -2.03 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1276 HIS 0.011 0.002 HIS B 450 PHE 0.024 0.002 PHE F 64 TYR 0.024 0.002 TYR B 349 ARG 0.006 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7064 (mtp) cc_final: 0.6497 (ttm) REVERT: B 303 VAL cc_start: 0.7556 (t) cc_final: 0.7346 (t) REVERT: B 372 MET cc_start: 0.7360 (mmm) cc_final: 0.6319 (mtt) REVERT: B 1169 THR cc_start: 0.3925 (m) cc_final: 0.3699 (m) REVERT: D 144 ILE cc_start: 0.8548 (tt) cc_final: 0.8348 (tt) REVERT: E 49 ILE cc_start: 0.9204 (pt) cc_final: 0.8801 (pt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.6438 time to fit residues: 254.0512 Evaluate side-chains 198 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS A 613 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN B 875 ASN B1218 HIS ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN F 81 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28889 Z= 0.268 Angle : 0.594 17.278 39430 Z= 0.316 Chirality : 0.041 0.163 4512 Planarity : 0.004 0.046 4824 Dihedral : 16.545 170.473 4859 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 40.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3338 helix: 0.98 (0.16), residues: 1141 sheet: -1.46 (0.24), residues: 453 loop : -1.85 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 9 HIS 0.006 0.001 HIS A 165 PHE 0.026 0.001 PHE F 65 TYR 0.022 0.002 TYR B 631 ARG 0.009 0.001 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6929 (mtp) cc_final: 0.6703 (ttm) REVERT: A 1180 MET cc_start: 0.7447 (ttp) cc_final: 0.7221 (ttm) REVERT: D 144 ILE cc_start: 0.8547 (tt) cc_final: 0.8347 (tt) REVERT: E 49 ILE cc_start: 0.9219 (pt) cc_final: 0.8816 (pt) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.6238 time to fit residues: 214.0119 Evaluate side-chains 174 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 8.9990 chunk 296 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 329 optimal weight: 7.9990 chunk 273 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.7562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28889 Z= 0.171 Angle : 0.500 13.383 39430 Z= 0.268 Chirality : 0.039 0.180 4512 Planarity : 0.003 0.051 4824 Dihedral : 16.348 170.051 4859 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 39.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.79 (0.15), residues: 3338 helix: 1.36 (0.16), residues: 1141 sheet: -1.32 (0.25), residues: 451 loop : -1.65 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 9 HIS 0.005 0.001 HIS F 33 PHE 0.013 0.001 PHE F 65 TYR 0.018 0.001 TYR B 631 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 MET cc_start: 0.7621 (ttp) cc_final: 0.7374 (ttm) REVERT: E 49 ILE cc_start: 0.9197 (pt) cc_final: 0.8769 (pt) REVERT: F 68 TYR cc_start: 0.6455 (m-80) cc_final: 0.6224 (m-10) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.6339 time to fit residues: 217.6995 Evaluate side-chains 172 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN B1367 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28889 Z= 0.206 Angle : 0.524 12.003 39430 Z= 0.280 Chirality : 0.039 0.143 4512 Planarity : 0.004 0.050 4824 Dihedral : 16.182 168.933 4859 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 41.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.15), residues: 3338 helix: 1.38 (0.16), residues: 1149 sheet: -1.29 (0.24), residues: 462 loop : -1.52 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 115 HIS 0.006 0.001 HIS B 450 PHE 0.024 0.001 PHE F 15 TYR 0.015 0.001 TYR A1305 ARG 0.005 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 MET cc_start: 0.7508 (ttp) cc_final: 0.7238 (ttm) REVERT: B 298 MET cc_start: 0.6226 (mtp) cc_final: 0.5921 (mtp) REVERT: D 142 MET cc_start: 0.5572 (ppp) cc_final: 0.5270 (ppp) REVERT: D 144 ILE cc_start: 0.8622 (tt) cc_final: 0.8414 (mt) REVERT: E 49 ILE cc_start: 0.9265 (pt) cc_final: 0.8692 (pt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.6295 time to fit residues: 207.5198 Evaluate side-chains 167 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 0.7980 chunk 131 optimal weight: 0.0970 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 chunk 223 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.8226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28889 Z= 0.122 Angle : 0.461 7.798 39430 Z= 0.247 Chirality : 0.039 0.141 4512 Planarity : 0.003 0.051 4824 Dihedral : 15.964 168.759 4859 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 37.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.29 (0.15), residues: 3338 helix: 1.72 (0.16), residues: 1142 sheet: -1.04 (0.25), residues: 440 loop : -1.31 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 997 HIS 0.004 0.001 HIS B 113 PHE 0.011 0.001 PHE F 65 TYR 0.011 0.001 TYR B1186 ARG 0.004 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7285 (tpt) cc_final: 0.7076 (tpt) REVERT: A 1180 MET cc_start: 0.7497 (ttp) cc_final: 0.7202 (ttm) REVERT: A 1243 MET cc_start: 0.8080 (tmm) cc_final: 0.7543 (tmm) REVERT: D 142 MET cc_start: 0.5641 (ppp) cc_final: 0.5323 (ppp) REVERT: E 48 VAL cc_start: 0.8614 (p) cc_final: 0.8407 (p) REVERT: E 49 ILE cc_start: 0.9130 (pt) cc_final: 0.8652 (pt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.6226 time to fit residues: 206.8502 Evaluate side-chains 171 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 0.9990 chunk 314 optimal weight: 0.2980 chunk 287 optimal weight: 0.0770 chunk 306 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 93 optimal weight: 0.0770 chunk 276 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28889 Z= 0.118 Angle : 0.454 6.780 39430 Z= 0.244 Chirality : 0.039 0.235 4512 Planarity : 0.003 0.054 4824 Dihedral : 15.805 168.206 4859 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 37.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.09 (0.15), residues: 3338 helix: 1.90 (0.16), residues: 1142 sheet: -0.97 (0.25), residues: 454 loop : -1.18 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 9 HIS 0.004 0.001 HIS B 113 PHE 0.017 0.001 PHE F 64 TYR 0.011 0.001 TYR B1186 ARG 0.007 0.000 ARG B1174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7275 (tpt) cc_final: 0.7042 (tpt) REVERT: A 1180 MET cc_start: 0.7492 (ttp) cc_final: 0.7196 (ttm) REVERT: A 1243 MET cc_start: 0.8018 (tmm) cc_final: 0.7407 (tmm) REVERT: D 224 LEU cc_start: 0.8262 (tt) cc_final: 0.8054 (tt) REVERT: E 49 ILE cc_start: 0.9141 (pt) cc_final: 0.8737 (pt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.5994 time to fit residues: 196.4588 Evaluate side-chains 166 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 chunk 312 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 805 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.8565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28889 Z= 0.171 Angle : 0.487 7.694 39430 Z= 0.261 Chirality : 0.039 0.154 4512 Planarity : 0.003 0.055 4824 Dihedral : 15.774 168.356 4859 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 40.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.12 (0.15), residues: 3338 helix: 1.85 (0.16), residues: 1142 sheet: -0.92 (0.25), residues: 456 loop : -1.20 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 9 HIS 0.003 0.001 HIS B 450 PHE 0.010 0.001 PHE F 65 TYR 0.013 0.001 TYR A1281 ARG 0.005 0.000 ARG B 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6676 Ramachandran restraints generated. 3338 Oldfield, 0 Emsley, 3338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7163 (tpt) cc_final: 0.6959 (tpt) REVERT: A 1180 MET cc_start: 0.7465 (ttp) cc_final: 0.7169 (ttm) REVERT: B 245 LEU cc_start: 0.7805 (tp) cc_final: 0.7600 (tp) REVERT: F 73 MET cc_start: 0.6516 (ppp) cc_final: 0.6299 (ppp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.6057 time to fit residues: 183.8980 Evaluate side-chains 165 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 0.6980 chunk 288 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 249 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.058826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040779 restraints weight = 381384.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042175 restraints weight = 193731.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.043080 restraints weight = 127598.649| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.8740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28889 Z= 0.150 Angle : 0.468 7.909 39430 Z= 0.251 Chirality : 0.039 0.135 4512 Planarity : 0.003 0.055 4824 Dihedral : 15.690 168.410 4859 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 39.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.03 (0.15), residues: 3338 helix: 1.92 (0.16), residues: 1142 sheet: -0.89 (0.25), residues: 464 loop : -1.14 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 9 HIS 0.003 0.001 HIS A 165 PHE 0.009 0.001 PHE B 49 TYR 0.016 0.001 TYR A1281 ARG 0.004 0.000 ARG E 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7628.58 seconds wall clock time: 140 minutes 35.98 seconds (8435.98 seconds total)