Starting phenix.real_space_refine on Fri Feb 23 20:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5o_27916/02_2024/8e5o_27916_neut.pdb" } resolution = 4.4 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 87 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17285 2.51 5 N 4941 2.21 5 O 5571 1.98 5 H 11229 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 GLU 892": "OE1" <-> "OE2" Residue "A GLU 898": "OE1" <-> "OE2" 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 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-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39229 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: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1031 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 464 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 15} 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: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1276 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 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 13860 SG CYS B 70 54.432 31.392 73.497 1.00 45.60 S ATOM 14119 SG CYS B 85 52.786 27.852 70.702 1.00 49.94 S ATOM 25701 SG CYS B 814 119.865 47.387 60.318 1.00 22.38 S ATOM 26838 SG CYS B 888 115.676 48.793 61.332 1.00 20.48 S ATOM 26929 SG CYS B 895 118.121 47.436 63.658 1.00 14.28 S ATOM 26966 SG CYS B 898 119.630 50.356 62.307 1.00 16.02 S Time building chain proxies: 18.63, per 1000 atoms: 0.47 Number of scatterers: 39229 At special positions: 0 Unit cell: (172.7, 139.7, 155.1, 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 87 15.00 Mg 1 11.99 O 5571 8.00 N 4941 7.00 C 17285 6.00 H 11229 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=2.27 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.87 Conformation dependent library (CDL) restraints added in 5.6 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 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6182 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 46 sheets defined 35.4% alpha, 15.1% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 16.78 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: 3.839A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.134A 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: 3.757A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.513A 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: 4.045A 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: 3.791A 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 942 through 979 Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.828A pdb=" N ASP A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 991 " --> pdb=" O LYS A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1005 through 1038 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.549A 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: 3.593A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.880A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 4.192A 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: 3.626A 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: 3.652A 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: 3.744A 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: 3.893A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.794A 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 286 removed outlier: 3.807A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 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: 3.549A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.690A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.568A 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: 3.648A 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: 3.522A 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: 3.612A 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: 3.644A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.532A 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: 3.643A 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: 3.520A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.193A 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: 3.544A 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: 3.827A 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: 4.421A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.549A 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: 3.839A 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: 4.041A 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: 3.525A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.685A 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 77 removed outlier: 3.956A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (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: 6.929A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR A 73 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.009A 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: 4.948A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.040A 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: 6.322A 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: 3.581A 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: 6.575A pdb=" N ALA A 257 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.965A 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: 3.688A 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: 5.946A 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: 3.688A 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: 4.895A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.669A 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: 3.994A 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: 3.591A 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: 9.206A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.536A 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: 3.863A pdb=" N GLY A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 843 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 830 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS A1057 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A 832 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A1055 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN A 834 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR A1053 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 836 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A1051 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 838 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A1049 " --> pdb=" O CYS A 838 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 840 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS A1057 " --> pdb=" O GLY A 926 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY A 926 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 926 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC2, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC3, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC4, 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: 6.652A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.873A 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: 6.518A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.415A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.686A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.802A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD4, 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: 3.710A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.088A 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=AD6, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD7, 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=AD8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.338A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AD9, 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=AE1, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.249A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.310A 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: 4.462A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE3, 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=AE4, 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: 4.349A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.074A 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: 4.263A 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=AE6, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE7, 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=AE8, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.625A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 39 through 43 removed outlier: 4.150A pdb=" N GLU F 41 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 72 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.684A pdb=" N GLU F 149 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.790A 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) 998 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 17.43 Time building geometry restraints manager: 27.09 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: 11214 1.03 - 1.23: 262 1.23 - 1.42: 11425 1.42 - 1.62: 16727 1.62 - 1.81: 203 Bond restraints: 39831 Sorted by residual: 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=" N1 G 7 33 " pdb=" H1 G 7 33 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" CA CYS B 70 " pdb=" CB CYS B 70 " ideal model delta sigma weight residual 1.527 1.405 0.122 1.38e-02 5.25e+03 7.84e+01 bond pdb=" C8 G 7 33 " pdb=" H8 G 7 33 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" N2 G 7 33 " pdb=" H22 G 7 33 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 39826 not shown) Histogram of bond angle deviations from ideal: 59.66 - 77.34: 2 77.34 - 95.01: 4 95.01 - 112.69: 36425 112.69 - 130.36: 28075 130.36 - 148.03: 122 Bond angle restraints: 64628 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 104.00 148.03 -44.03 1.50e+00 4.44e-01 8.62e+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 76.06 32.94 1.50e+00 4.44e-01 4.82e+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 59.66 48.34 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C VAL A 920 " pdb=" N PRO A 921 " pdb=" CA PRO A 921 " ideal model delta sigma weight residual 119.84 139.49 -19.65 1.25e+00 6.40e-01 2.47e+02 angle pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " pdb=" O5' DT 6 29 " ideal model delta sigma weight residual 104.00 126.05 -22.05 1.50e+00 4.44e-01 2.16e+02 ... (remaining 64623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19935 35.99 - 71.98: 830 71.98 - 107.97: 18 107.97 - 143.96: 1 143.96 - 179.95: 7 Dihedral angle restraints: 20791 sinusoidal: 10766 harmonic: 10025 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 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 27 " pdb=" C1' U 7 27 " pdb=" N1 U 7 27 " pdb=" C2 U 7 27 " ideal model delta sinusoidal sigma weight residual 200.00 43.60 156.40 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 -138.14 -41.86 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 20788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4023 0.107 - 0.215: 402 0.215 - 0.322: 24 0.322 - 0.430: 2 0.430 - 0.537: 2 Chirality restraints: 4453 Sorted by residual: 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 2.11 0.54 2.00e-01 2.50e+01 7.21e+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 4.88e+00 chirality pdb=" CB ILE A 765 " pdb=" CA ILE A 765 " pdb=" CG1 ILE A 765 " pdb=" CG2 ILE A 765 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 4450 not shown) Planarity restraints: 6121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.210 2.00e-02 2.50e+03 2.51e-01 9.43e+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 ILE B 61 " 0.029 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" N PHE B 62 " -0.098 2.00e-02 2.50e+03 pdb=" CA PHE B 62 " 0.023 2.00e-02 2.50e+03 pdb=" H PHE B 62 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 69 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLU B 69 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 69 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS B 70 " 0.029 2.00e-02 2.50e+03 ... (remaining 6118 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 253 1.89 - 2.57: 22968 2.57 - 3.24: 82378 3.24 - 3.92: 118929 3.92 - 4.60: 180864 Nonbonded interactions: 405392 Sorted by model distance: nonbonded pdb=" O3' DA 5 103 " pdb=" NH2 ARG A 473 " model vdw 1.211 2.350 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 38 " model vdw 1.266 2.100 nonbonded pdb=" HA LYS B 222 " pdb=" HD2 LYS B 222 " model vdw 1.325 2.440 nonbonded pdb=" OE2 GLU A 641 " pdb=" HZ3 LYS B 749 " model vdw 1.339 1.850 nonbonded pdb=" HG2 ARG B 202 " pdb="HH11 ARG B 202 " model vdw 1.347 2.270 ... (remaining 405387 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: 0.010 Normalize map: mean=0, sd=1: 2.710 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: 0.710 Extract box with map and model: 13.780 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 132.280 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4293 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 0.164 28602 Z= 0.635 Angle : 1.169 48.337 39002 Z= 0.667 Chirality : 0.065 0.537 4453 Planarity : 0.007 0.081 4803 Dihedral : 15.493 156.396 11233 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.77 % Favored : 90.53 % Rotamer: Outliers : 4.25 % Allowed : 4.35 % Favored : 91.40 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -4.35 (0.11), residues: 3328 helix: -2.91 (0.11), residues: 1100 sheet: -2.01 (0.24), residues: 401 loop : -3.17 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 PHE 0.035 0.003 PHE B 620 TYR 0.038 0.003 TYR A1229 ARG 0.013 0.001 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 347 time to evaluate : 3.855 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: A 492 MET cc_start: 0.6475 (mtm) cc_final: 0.6195 (tpp) REVERT: A 896 THR cc_start: -0.5724 (OUTLIER) cc_final: -0.5939 (m) REVERT: A 905 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3997 (mp) REVERT: A 920 VAL cc_start: -0.0397 (OUTLIER) cc_final: -0.0786 (m) REVERT: A 990 ASP cc_start: 0.6523 (p0) cc_final: 0.5896 (t0) REVERT: A 1230 MET cc_start: 0.6084 (ttm) cc_final: 0.5475 (ttt) REVERT: A 1337 ILE cc_start: 0.4637 (tt) cc_final: 0.4346 (tt) REVERT: B 70 CYS cc_start: 0.3558 (OUTLIER) cc_final: 0.3117 (t) REVERT: B 132 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5833 (tt) REVERT: B 154 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5614 (mp) REVERT: B 222 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6783 (tppt) REVERT: C 142 MET cc_start: 0.3837 (ptp) cc_final: 0.3224 (ptm) REVERT: D 82 LEU cc_start: 0.7031 (mt) cc_final: 0.6711 (tt) REVERT: F 176 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.6623 (p) outliers start: 121 outliers final: 37 residues processed: 456 average time/residue: 0.6920 time to fit residues: 481.6003 Evaluate side-chains 242 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 0.0270 chunk 198 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 437 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 618 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN A1313 HIS B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 GLN C 37 HIS C 147 GLN D 66 HIS D 117 HIS D 127 GLN D 227 GLN F 33 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 28602 Z= 0.160 Angle : 0.568 8.874 39002 Z= 0.308 Chirality : 0.041 0.195 4453 Planarity : 0.005 0.055 4803 Dihedral : 15.858 149.499 4686 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % 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: -2.66 (0.13), residues: 3328 helix: -0.57 (0.14), residues: 1113 sheet: -1.77 (0.25), residues: 417 loop : -2.64 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.007 0.001 HIS B 777 PHE 0.017 0.001 PHE B 141 TYR 0.014 0.001 TYR F 153 ARG 0.006 0.000 ARG B 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 3.762 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: A 68 LEU cc_start: 0.5821 (mt) cc_final: 0.5596 (mt) REVERT: A 990 ASP cc_start: 0.6712 (p0) cc_final: 0.6168 (t0) REVERT: B 242 LEU cc_start: 0.5299 (tt) cc_final: 0.5071 (tt) REVERT: B 513 MET cc_start: 0.4563 (tmm) cc_final: 0.3789 (tmm) REVERT: B 1095 MET cc_start: 0.0086 (ttt) cc_final: -0.0647 (ttt) REVERT: F 133 MET cc_start: 0.5190 (tpp) cc_final: 0.4268 (tpt) outliers start: 2 outliers final: 1 residues processed: 232 average time/residue: 0.6149 time to fit residues: 226.4881 Evaluate side-chains 176 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 0.1980 chunk 256 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 309 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS A1061 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4699 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 28602 Z= 0.140 Angle : 0.498 9.025 39002 Z= 0.269 Chirality : 0.040 0.144 4453 Planarity : 0.004 0.075 4803 Dihedral : 15.479 147.664 4686 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.37 % Favored : 93.45 % Rotamer: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.65 (0.14), residues: 3328 helix: 0.73 (0.16), residues: 1098 sheet: -1.55 (0.24), residues: 444 loop : -2.26 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 80 HIS 0.005 0.001 HIS A 273 PHE 0.026 0.001 PHE B 116 TYR 0.010 0.001 TYR B 679 ARG 0.009 0.000 ARG F 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 3.491 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: A 369 MET cc_start: 0.4844 (ttm) cc_final: 0.4270 (ttp) REVERT: A 990 ASP cc_start: 0.6498 (p0) cc_final: 0.6182 (p0) REVERT: A 1329 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6278 (tt0) REVERT: B 697 MET cc_start: 0.6977 (ptm) cc_final: 0.6681 (ptt) REVERT: B 1095 MET cc_start: -0.1050 (ttt) cc_final: -0.2023 (ttt) REVERT: D 82 LEU cc_start: 0.6890 (mt) cc_final: 0.6544 (pp) REVERT: F 73 MET cc_start: 0.1140 (tpt) cc_final: 0.0929 (tpp) REVERT: F 133 MET cc_start: 0.5486 (tpp) cc_final: 0.4908 (tpt) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.5813 time to fit residues: 200.1863 Evaluate side-chains 166 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 328 optimal weight: 0.0060 chunk 162 optimal weight: 0.0570 chunk 294 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** 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 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 808 ASN A1061 GLN A1136 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 921 GLN B1244 GLN B1259 GLN B1367 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28602 Z= 0.304 Angle : 0.764 23.517 39002 Z= 0.401 Chirality : 0.045 0.243 4453 Planarity : 0.006 0.061 4803 Dihedral : 15.647 144.559 4686 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 46.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.93 % Favored : 91.92 % Rotamer: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: 3328 helix: 0.36 (0.15), residues: 1128 sheet: -1.57 (0.24), residues: 446 loop : -2.11 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1276 HIS 0.011 0.002 HIS B 865 PHE 0.039 0.003 PHE A1270 TYR 0.026 0.002 TYR A 291 ARG 0.010 0.001 ARG A 647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 3.682 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: A 685 MET cc_start: 0.8075 (mtm) cc_final: 0.7725 (mtm) REVERT: A 1151 LEU cc_start: 0.7361 (tp) cc_final: 0.6608 (tp) REVERT: B 697 MET cc_start: 0.7234 (ptm) cc_final: 0.6544 (ptp) REVERT: B 1095 MET cc_start: -0.1939 (ttt) cc_final: -0.2209 (ttt) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.5399 time to fit residues: 172.7943 Evaluate side-chains 141 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 613 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN A1324 ASN B 300 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 1.0001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28602 Z= 0.346 Angle : 0.805 19.475 39002 Z= 0.427 Chirality : 0.046 0.242 4453 Planarity : 0.006 0.125 4803 Dihedral : 15.992 138.731 4686 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 50.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.11 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -2.06 (0.14), residues: 3328 helix: -0.08 (0.15), residues: 1138 sheet: -1.72 (0.23), residues: 450 loop : -2.19 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 80 HIS 0.011 0.002 HIS B1227 PHE 0.039 0.003 PHE B 116 TYR 0.023 0.003 TYR A 62 ARG 0.017 0.001 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.626 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: A 320 ASP cc_start: 0.7716 (t0) cc_final: 0.7506 (t0) REVERT: A 515 MET cc_start: 0.8669 (tmm) cc_final: 0.8378 (tmm) REVERT: A 1151 LEU cc_start: 0.7716 (tp) cc_final: 0.7379 (tp) REVERT: A 1304 MET cc_start: 0.6657 (mmp) cc_final: 0.6417 (mmp) REVERT: B 697 MET cc_start: 0.7567 (ptm) cc_final: 0.7130 (ppp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.5558 time to fit residues: 138.0481 Evaluate side-chains 118 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 328 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 1.0466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28602 Z= 0.198 Angle : 0.566 17.906 39002 Z= 0.301 Chirality : 0.040 0.146 4453 Planarity : 0.004 0.065 4803 Dihedral : 15.605 133.075 4686 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 42.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -1.57 (0.14), residues: 3328 helix: 0.56 (0.15), residues: 1141 sheet: -1.61 (0.24), residues: 442 loop : -2.05 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 9 HIS 0.006 0.001 HIS B 865 PHE 0.022 0.001 PHE B 116 TYR 0.013 0.001 TYR B1282 ARG 0.008 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.658 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: A 653 MET cc_start: 0.6768 (tpt) cc_final: 0.6362 (tpt) REVERT: A 685 MET cc_start: 0.7744 (mtm) cc_final: 0.7417 (mtm) REVERT: A 1151 LEU cc_start: 0.7784 (tp) cc_final: 0.7458 (tp) REVERT: B 697 MET cc_start: 0.7499 (ptm) cc_final: 0.7115 (ppp) REVERT: D 205 MET cc_start: 0.7858 (ppp) cc_final: 0.7619 (ppp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5812 time to fit residues: 133.1778 Evaluate side-chains 114 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.0050 chunk 37 optimal weight: 0.0270 chunk 187 optimal weight: 7.9990 chunk 240 optimal weight: 0.0570 chunk 186 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 overall best weight: 0.3570 ------------------------------------------------------------------------------- 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 604 HIS A 628 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 1.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28602 Z= 0.121 Angle : 0.466 7.581 39002 Z= 0.250 Chirality : 0.039 0.145 4453 Planarity : 0.004 0.055 4803 Dihedral : 15.310 122.850 4686 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 34.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -0.86 (0.15), residues: 3328 helix: 1.33 (0.16), residues: 1142 sheet: -1.37 (0.24), residues: 454 loop : -1.72 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 115 HIS 0.007 0.001 HIS B 113 PHE 0.021 0.001 PHE B 116 TYR 0.010 0.001 TYR B 589 ARG 0.004 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.500 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: A 653 MET cc_start: 0.6770 (tpt) cc_final: 0.6373 (tpt) REVERT: A 685 MET cc_start: 0.7632 (mtm) cc_final: 0.7261 (mtm) REVERT: A 1151 LEU cc_start: 0.7637 (tp) cc_final: 0.7206 (tp) REVERT: B 697 MET cc_start: 0.7541 (ptm) cc_final: 0.7030 (ppp) REVERT: F 133 MET cc_start: 0.4370 (tpt) cc_final: 0.3943 (tpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.5465 time to fit residues: 123.5497 Evaluate side-chains 115 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 98 optimal weight: 0.0170 chunk 64 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 1.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28602 Z= 0.113 Angle : 0.447 6.467 39002 Z= 0.240 Chirality : 0.039 0.144 4453 Planarity : 0.003 0.056 4803 Dihedral : 15.091 109.259 4686 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 34.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3328 helix: 1.71 (0.16), residues: 1140 sheet: -1.15 (0.24), residues: 454 loop : -1.56 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.003 0.000 HIS B 104 PHE 0.012 0.001 PHE B 620 TYR 0.010 0.001 TYR A 291 ARG 0.004 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.999 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: A 653 MET cc_start: 0.6936 (tpt) cc_final: 0.6587 (tpt) REVERT: A 685 MET cc_start: 0.7749 (mtm) cc_final: 0.7457 (mtm) REVERT: A 1304 MET cc_start: 0.6391 (mmp) cc_final: 0.5968 (mmp) REVERT: B 115 TRP cc_start: 0.5215 (m100) cc_final: 0.5002 (m100) REVERT: B 242 LEU cc_start: 0.6036 (tt) cc_final: 0.5810 (tt) REVERT: B 697 MET cc_start: 0.7593 (ptm) cc_final: 0.7168 (ppp) REVERT: F 133 MET cc_start: 0.5253 (tpt) cc_final: 0.4915 (tpt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5599 time to fit residues: 126.0078 Evaluate side-chains 116 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 286 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 93 optimal weight: 0.0170 chunk 275 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 304 optimal weight: 0.0870 overall best weight: 3.2202 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN A 688 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 1.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28602 Z= 0.262 Angle : 0.623 11.783 39002 Z= 0.331 Chirality : 0.041 0.165 4453 Planarity : 0.004 0.065 4803 Dihedral : 15.292 101.064 4686 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 47.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % 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: -0.99 (0.14), residues: 3328 helix: 1.07 (0.15), residues: 1141 sheet: -1.46 (0.24), residues: 434 loop : -1.67 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 9 HIS 0.008 0.001 HIS B 865 PHE 0.023 0.002 PHE F 65 TYR 0.016 0.002 TYR B 589 ARG 0.010 0.001 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.573 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: A 653 MET cc_start: 0.6912 (tpt) cc_final: 0.6695 (tpt) REVERT: A 1151 LEU cc_start: 0.7750 (tp) cc_final: 0.7426 (tp) REVERT: B 242 LEU cc_start: 0.6413 (tt) cc_final: 0.6123 (tt) REVERT: B 697 MET cc_start: 0.7679 (ptm) cc_final: 0.7146 (ppp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.5620 time to fit residues: 122.5092 Evaluate side-chains 113 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 338 optimal weight: 3.9990 chunk 311 optimal weight: 0.0010 chunk 269 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 GLN ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 1.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28602 Z= 0.121 Angle : 0.476 11.654 39002 Z= 0.253 Chirality : 0.039 0.143 4453 Planarity : 0.004 0.076 4803 Dihedral : 15.074 97.210 4686 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 37.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3328 helix: 1.66 (0.16), residues: 1134 sheet: -1.16 (0.24), residues: 460 loop : -1.52 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 115 HIS 0.003 0.000 HIS B 777 PHE 0.011 0.001 PHE B 62 TYR 0.010 0.001 TYR B 589 ARG 0.006 0.000 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.072 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: A 369 MET cc_start: 0.6587 (tpt) cc_final: 0.6274 (tpt) REVERT: A 1304 MET cc_start: 0.6544 (mmp) cc_final: 0.6325 (mmp) REVERT: B 242 LEU cc_start: 0.6370 (tt) cc_final: 0.6078 (tt) REVERT: B 697 MET cc_start: 0.7572 (ptm) cc_final: 0.7215 (ppp) REVERT: E 68 GLU cc_start: 0.8100 (pt0) cc_final: 0.7892 (pt0) REVERT: F 133 MET cc_start: 0.4472 (tpt) cc_final: 0.4147 (tpt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5921 time to fit residues: 130.4426 Evaluate side-chains 115 residues out of total 2857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.042491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031432 restraints weight = 752546.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.032379 restraints weight = 473763.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.033054 restraints weight = 343071.655| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 1.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28602 Z= 0.155 Angle : 0.487 8.088 39002 Z= 0.260 Chirality : 0.039 0.143 4453 Planarity : 0.004 0.072 4803 Dihedral : 15.003 97.287 4686 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 40.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3328 helix: 1.75 (0.16), residues: 1134 sheet: -1.26 (0.24), residues: 448 loop : -1.42 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 115 HIS 0.005 0.001 HIS B 865 PHE 0.011 0.001 PHE F 65 TYR 0.012 0.001 TYR B 589 ARG 0.029 0.000 ARG B1174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6893.83 seconds wall clock time: 127 minutes 11.05 seconds (7631.05 seconds total)