Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 01:49:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/08_2023/8e6z_27931_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/08_2023/8e6z_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_27931/08_2023/8e6z_27931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/08_2023/8e6z_27931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/08_2023/8e6z_27931_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6z_27931/08_2023/8e6z_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 17.94, per 1000 atoms: 0.45 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: 27.89 Conformation dependent library (CDL) restraints added in 4.5 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: 16.21 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: 19.23 Time building geometry restraints manager: 28.60 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: 18677 35.99 - 71.98: 639 71.98 - 107.97: 28 107.97 - 143.96: 2 143.96 - 179.95: 9 Dihedral angle restraints: 19355 sinusoidal: 9309 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 19352 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: 3.100 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: 0.830 Extract box with map and model: 16.230 Check model and map are aligned: 0.680 Set scattering table: 0.370 Process input model: 139.500 Find NCS groups from input model: 1.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.830 ------------------------------------------------------------------------------- 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 : 15.548 163.715 11255 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 % 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 *********************** 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 : 3.666 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 outliers start: 123 outliers final: 28 residues processed: 643 average time/residue: 0.7316 time to fit residues: 710.6317 Evaluate side-chains 315 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6762 time to fit residues: 34.6078 ------------------------------------------------------------------------------- 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: 5.9990 chunk 143 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 267 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 686 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 28889 Z= 0.181 Angle : 0.584 8.431 39430 Z= 0.316 Chirality : 0.041 0.153 4512 Planarity : 0.005 0.054 4824 Dihedral : 15.779 170.008 4689 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.02 % Favored : 93.77 % Rotamer Outliers : 0.18 % 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: -2.69 (0.13), residues: 3338 helix: -0.59 (0.15), residues: 1112 sheet: -2.03 (0.23), residues: 458 loop : -2.58 (0.13), residues: 1768 *********************** 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 343 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 3.794 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 outliers start: 5 outliers final: 2 residues processed: 343 average time/residue: 0.6535 time to fit residues: 350.5103 Evaluate side-chains 243 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 3.700 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3783 time to fit residues: 6.1702 ------------------------------------------------------------------------------- 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: 5.9990 chunk 96 optimal weight: 8.9990 chunk 257 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 276 optimal weight: 0.3980 chunk 307 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 248 optimal weight: 0.3980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 238 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 437 ASN A 628 HIS A 808 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 651 HIS ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** 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** E 29 GLN F 33 HIS ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 28889 Z= 0.369 Angle : 0.736 20.771 39430 Z= 0.391 Chirality : 0.043 0.199 4512 Planarity : 0.005 0.062 4824 Dihedral : 15.744 170.854 4689 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 37.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.94 % Favored : 91.91 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.90 (0.14), residues: 3338 helix: 0.35 (0.15), residues: 1124 sheet: -1.77 (0.23), residues: 464 loop : -2.28 (0.14), residues: 1750 *********************** 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 274 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 4.155 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 outliers start: 4 outliers final: 2 residues processed: 274 average time/residue: 0.6319 time to fit residues: 274.5616 Evaluate side-chains 213 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4050 time to fit residues: 6.1793 ------------------------------------------------------------------------------- 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: 2.9990 chunk 233 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 28889 Z= 0.241 Angle : 0.565 13.407 39430 Z= 0.304 Chirality : 0.040 0.188 4512 Planarity : 0.004 0.053 4824 Dihedral : 15.536 170.466 4689 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 36.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.56 % Favored : 93.26 % Rotamer Outliers : 0.04 % 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: -1.37 (0.14), residues: 3338 helix: 0.94 (0.16), residues: 1133 sheet: -1.68 (0.24), residues: 452 loop : -2.01 (0.14), residues: 1753 *********************** 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: 1 poor density : 251 time to evaluate : 4.083 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 outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.6457 time to fit residues: 259.7037 Evaluate side-chains 192 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0007 ------------------------------------------------------------------------------- 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: 5.9990 chunk 187 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 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 604 HIS ** A 613 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** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 875 ASN B1367 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 23 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** F 81 HIS ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 28889 Z= 0.382 Angle : 0.724 13.672 39430 Z= 0.381 Chirality : 0.043 0.188 4512 Planarity : 0.005 0.058 4824 Dihedral : 15.692 171.173 4689 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 48.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.90 % Favored : 90.95 % Rotamer Outliers : 0.00 % 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: -1.68 (0.14), residues: 3338 helix: 0.38 (0.15), residues: 1141 sheet: -1.61 (0.24), residues: 433 loop : -2.06 (0.14), residues: 1764 *********************** 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 209 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.879 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 outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.6324 time to fit residues: 213.3584 Evaluate side-chains 162 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1535 ------------------------------------------------------------------------------- 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: 1.9990 chunk 296 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 613 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1218 HIS ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** 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: 0.6942 moved from start: 0.7790 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= 0.148 Angle : 0.496 9.646 39430 Z= 0.268 Chirality : 0.039 0.154 4512 Planarity : 0.003 0.049 4824 Dihedral : 15.412 171.117 4689 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 38.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer Outliers : 0.00 % 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: -1.00 (0.15), residues: 3338 helix: 1.19 (0.16), residues: 1142 sheet: -1.43 (0.25), residues: 442 loop : -1.78 (0.14), residues: 1754 *********************** 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 207 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.689 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 outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.6109 time to fit residues: 203.9524 Evaluate side-chains 168 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 4.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4218 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 238 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 450 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** 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** ** C 18 GLN ** 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 117 HIS ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.8856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 28889 Z= 0.403 Angle : 0.742 12.286 39430 Z= 0.391 Chirality : 0.043 0.195 4512 Planarity : 0.005 0.056 4824 Dihedral : 15.644 172.299 4689 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 53.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.80 % Favored : 89.96 % Rotamer Outliers : 0.00 % 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: -1.73 (0.14), residues: 3338 helix: 0.33 (0.15), residues: 1125 sheet: -1.63 (0.24), residues: 451 loop : -2.06 (0.14), residues: 1762 *********************** 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 188 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 3.596 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 outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.6267 time to fit residues: 190.4189 Evaluate side-chains 155 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9866 ------------------------------------------------------------------------------- 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: 1.9990 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 99 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 117 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 28889 Z= 0.167 Angle : 0.513 11.794 39430 Z= 0.277 Chirality : 0.040 0.168 4512 Planarity : 0.003 0.048 4824 Dihedral : 15.338 172.034 4689 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 41.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer Outliers : 0.00 % 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: -1.16 (0.15), residues: 3338 helix: 1.00 (0.16), residues: 1143 sheet: -1.50 (0.25), residues: 454 loop : -1.84 (0.14), residues: 1741 *********************** 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 193 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 4.314 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 outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.6530 time to fit residues: 203.4282 Evaluate side-chains 156 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7866 ------------------------------------------------------------------------------- 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: 0.6980 chunk 314 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 93 optimal weight: 0.0060 chunk 276 optimal weight: 0.0170 chunk 289 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.1236 ------------------------------------------------------------------------------- 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 238 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** B1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.8986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 28889 Z= 0.151 Angle : 0.489 8.247 39430 Z= 0.262 Chirality : 0.039 0.155 4512 Planarity : 0.003 0.046 4824 Dihedral : 15.051 171.677 4689 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 40.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.64 % Favored : 92.27 % Rotamer Outliers : 0.00 % 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: -0.78 (0.15), residues: 3338 helix: 1.42 (0.16), residues: 1149 sheet: -1.45 (0.24), residues: 465 loop : -1.65 (0.15), residues: 1724 *********************** 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 198 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.905 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 outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.6324 time to fit residues: 201.1966 Evaluate side-chains 156 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6120 ------------------------------------------------------------------------------- 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: 5.9990 chunk 323 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 339 optimal weight: 8.9990 chunk 312 optimal weight: 0.5980 chunk 270 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 238 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 437 ASN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 805 GLN ** B1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** 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: 0.7016 moved from start: 0.9090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 28889 Z= 0.139 Angle : 0.472 7.543 39430 Z= 0.254 Chirality : 0.039 0.154 4512 Planarity : 0.003 0.045 4824 Dihedral : 14.877 171.254 4689 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 40.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.04 % Favored : 92.87 % Rotamer Outliers : 0.00 % 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: -0.53 (0.15), residues: 3338 helix: 1.67 (0.16), residues: 1149 sheet: -1.31 (0.25), residues: 450 loop : -1.54 (0.15), residues: 1739 ********************** 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 : 3.784 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.6407 time to fit residues: 196.2924 Evaluate side-chains 161 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7348 ------------------------------------------------------------------------------- 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: 4.9990 chunk 288 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 238 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** B1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.055977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038154 restraints weight = 398512.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.039501 restraints weight = 197681.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.040341 restraints weight = 129818.049| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.9527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 28889 Z= 0.291 Angle : 0.597 8.410 39430 Z= 0.318 Chirality : 0.040 0.156 4512 Planarity : 0.004 0.044 4824 Dihedral : 15.034 172.297 4689 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 47.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.14 % Favored : 90.77 % Rotamer Outliers : 0.00 % 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: -0.90 (0.15), residues: 3338 helix: 1.22 (0.16), residues: 1136 sheet: -1.29 (0.25), residues: 439 loop : -1.70 (0.14), residues: 1763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7466.80 seconds wall clock time: 136 minutes 2.80 seconds (8162.80 seconds total)