Starting phenix.real_space_refine on Fri Dec 15 04:55:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/12_2023/6n58_0349_trim_updated.pdb" } resolution = 3.78 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 Mg 1 5.21 5 S 137 5.16 5 C 18938 2.51 5 N 5317 2.21 5 O 5793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30189 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} 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: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10479 Classifications: {'peptide': 1347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1290} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4379 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 527} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" 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} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14479 SG CYS J 70 50.636 39.118 118.330 1.00 42.49 S ATOM 14493 SG CYS J 72 52.456 36.933 120.146 1.00 40.35 S ATOM 14601 SG CYS J 85 49.125 37.546 121.088 1.00 45.47 S ATOM 14625 SG CYS J 88 52.028 41.325 120.599 1.00 44.20 S ATOM 20313 SG CYS J 814 25.028 89.891 83.027 1.00 30.79 S ATOM 20878 SG CYS J 888 28.202 88.922 84.710 1.00 35.98 S ATOM 20929 SG CYS J 895 27.227 87.732 81.641 1.00 21.07 S ATOM 20950 SG CYS J 898 27.929 90.922 80.740 1.00 20.11 S ATOM 29787 SG CYS M 37 75.580 130.033 82.388 1.00 48.55 S ATOM 29807 SG CYS M 40 78.608 131.974 83.105 1.00 49.34 S ATOM 29944 SG CYS M 58 80.141 129.281 81.623 1.00 45.33 S ATOM 29966 SG CYS M 61 78.215 128.768 84.493 1.00 42.90 S Time building chain proxies: 16.10, per 1000 atoms: 0.53 Number of scatterers: 30189 At special positions: 0 Unit cell: (153.4, 159.9, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 137 16.00 Mg 1 11.99 O 5793 8.00 N 5317 7.00 C 18938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.07 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 58 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 61 " Number of angles added : 18 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 31 sheets defined 37.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 85 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 85 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 227 removed outlier: 4.402A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 87 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.552A pdb=" N ILE I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.529A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 292 No H-bonds generated for 'chain 'I' and resid 289 through 292' Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.520A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.873A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 407 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.016A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 545 through 548 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 686 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.634A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 995 through 997 No H-bonds generated for 'chain 'I' and resid 995 through 997' Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1100 through 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.750A pdb=" N LYS I1133 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1139 through 1150 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1166 through 1176 removed outlier: 3.764A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1186 through 1188 No H-bonds generated for 'chain 'I' and resid 1186 through 1188' Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1273 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.501A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 116 No H-bonds generated for 'chain 'J' and resid 114 through 116' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 140 Processing helix chain 'J' and resid 162 through 171 removed outlier: 4.012A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.108A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 457 removed outlier: 3.904A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 removed outlier: 3.799A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 removed outlier: 3.533A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 648 through 669 removed outlier: 4.132A pdb=" N HIS J 651 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 788 removed outlier: 4.192A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 792 No H-bonds generated for 'chain 'J' and resid 790 through 792' Processing helix chain 'J' and resid 795 through 801 Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 3.927A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1071 No H-bonds generated for 'chain 'J' and resid 1069 through 1071' Processing helix chain 'J' and resid 1139 through 1145 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.273A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1262 removed outlier: 4.010A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1319 through 1325 removed outlier: 3.773A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1352 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.529A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 79 Processing helix chain 'L' and resid 8 through 19 Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 38 through 51 removed outlier: 3.705A pdb=" N MET L 51 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 89 removed outlier: 4.789A pdb=" N SER L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 116 through 135 Processing helix chain 'L' and resid 138 through 153 Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 245 through 258 removed outlier: 4.914A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 291 removed outlier: 3.703A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 306 removed outlier: 3.728A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 320 No H-bonds generated for 'chain 'L' and resid 317 through 320' Processing helix chain 'L' and resid 330 through 351 removed outlier: 3.734A pdb=" N SER L 334 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU L 335 " --> pdb=" O ASP L 332 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU L 336 " --> pdb=" O VAL L 333 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS L 343 " --> pdb=" O ALA L 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 394 removed outlier: 5.335A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 removed outlier: 4.413A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 473 removed outlier: 3.738A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 removed outlier: 4.075A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 521 No H-bonds generated for 'chain 'L' and resid 519 through 521' Processing helix chain 'L' and resid 531 through 550 Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 579 Processing helix chain 'L' and resid 585 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 4 through 26 removed outlier: 3.793A pdb=" N ALA M 8 " --> pdb=" O GLU M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 51 Processing helix chain 'M' and resid 59 through 70 Processing sheet with id= A, first strand: chain 'G' and resid 23 through 28 Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.927A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.538A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 188 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 202 " --> pdb=" O ASN H 186 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.184A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.761A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 66 through 69 removed outlier: 3.606A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= I, first strand: chain 'I' and resid 154 through 158 Processing sheet with id= J, first strand: chain 'I' and resid 184 through 188 Processing sheet with id= K, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= L, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= M, first strand: chain 'I' and resid 589 through 592 Processing sheet with id= N, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= O, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.865A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 798 through 804 removed outlier: 4.244A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 830 through 832 Processing sheet with id= R, first strand: chain 'I' and resid 835 through 838 removed outlier: 3.861A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= T, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= U, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.415A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.779A pdb=" N LEU J 242 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.868A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 365 through 369 removed outlier: 5.726A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 434 through 437 Processing sheet with id= Z, first strand: chain 'J' and resid 548 through 550 Processing sheet with id= AA, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AB, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AC, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AD, first strand: chain 'J' and resid 1161 through 1165 removed outlier: 4.160A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.639A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.85 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10273 1.34 - 1.46: 6173 1.46 - 1.59: 13925 1.59 - 1.71: 16 1.71 - 1.84: 247 Bond restraints: 30634 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.836 -0.304 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C19 1N7 L 702 " pdb=" C3 1N7 L 702 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C19 1N7 M 102 " pdb=" C3 1N7 M 102 " ideal model delta sigma weight residual 1.532 1.809 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.724 -0.192 2.00e-02 2.50e+03 9.25e+01 ... (remaining 30629 not shown) Histogram of bond angle deviations from ideal: 95.49 - 105.12: 619 105.12 - 114.76: 18802 114.76 - 124.39: 21534 124.39 - 134.02: 423 134.02 - 143.66: 5 Bond angle restraints: 41383 Sorted by residual: angle pdb=" C THR J1024 " pdb=" N MET J1025 " pdb=" CA MET J1025 " ideal model delta sigma weight residual 121.80 143.66 -21.86 2.44e+00 1.68e-01 8.02e+01 angle pdb=" C LEU G 9 " pdb=" N LYS G 10 " pdb=" CA LYS G 10 " ideal model delta sigma weight residual 122.38 100.60 21.78 2.90e+00 1.19e-01 5.64e+01 angle pdb=" C ASP J1094 " pdb=" N MET J1095 " pdb=" CA MET J1095 " ideal model delta sigma weight residual 122.28 133.93 -11.65 1.77e+00 3.19e-01 4.33e+01 angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.86 131.33 -10.47 1.60e+00 3.91e-01 4.28e+01 angle pdb=" N VAL H 192 " pdb=" CA VAL H 192 " pdb=" C VAL H 192 " ideal model delta sigma weight residual 110.21 103.80 6.41 1.13e+00 7.83e-01 3.22e+01 ... (remaining 41378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.48: 18392 19.48 - 38.96: 682 38.96 - 58.44: 47 58.44 - 77.91: 31 77.91 - 97.39: 3 Dihedral angle restraints: 19155 sinusoidal: 8111 harmonic: 11044 Sorted by residual: dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 134.70 45.30 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA ASP I 199 " pdb=" C ASP I 199 " pdb=" N ARG I 200 " pdb=" CA ARG I 200 " ideal model delta harmonic sigma weight residual -180.00 -135.57 -44.43 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA GLN I1134 " pdb=" C GLN I1134 " pdb=" N GLN I1135 " pdb=" CA GLN I1135 " ideal model delta harmonic sigma weight residual -180.00 -138.86 -41.14 0 5.00e+00 4.00e-02 6.77e+01 ... (remaining 19152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3744 0.072 - 0.144: 911 0.144 - 0.216: 77 0.216 - 0.288: 8 0.288 - 0.360: 4 Chirality restraints: 4744 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C19 1N7 M 102 " pdb=" C18 1N7 M 102 " pdb=" C2 1N7 M 102 " pdb=" C3 1N7 M 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.88 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C5 1N7 M 102 " pdb=" C4 1N7 M 102 " pdb=" C6 1N7 M 102 " pdb=" C9 1N7 M 102 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 4741 not shown) Planarity restraints: 5404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO J 246 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO J 247 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO J 247 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 247 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 59 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO L 60 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO I 560 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " 0.047 5.00e-02 4.00e+02 ... (remaining 5401 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 226 2.49 - 3.10: 25426 3.10 - 3.70: 43572 3.70 - 4.30: 64326 4.30 - 4.90: 105690 Nonbonded interactions: 239240 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 1.892 2.170 nonbonded pdb=" OD1 ASP I 516 " pdb=" OG SER I 522 " model vdw 1.918 2.440 nonbonded pdb=" OG SER J1057 " pdb=" OE2 GLU J1110 " model vdw 1.941 2.440 nonbonded pdb=" O LYS G 104 " pdb=" OG SER G 139 " model vdw 2.028 2.440 nonbonded pdb=" O GLU J 204 " pdb=" OG1 THR J 208 " model vdw 2.041 2.440 ... (remaining 239235 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 'G' and (resid 8 through 158 or resid 171 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 8 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.030 Extract box with map and model: 5.530 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 85.730 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.013 0.304 30634 Z= 0.873 Angle : 1.211 21.856 41383 Z= 0.660 Chirality : 0.060 0.360 4744 Planarity : 0.007 0.100 5404 Dihedral : 10.750 97.393 12033 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 38.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.66 % Favored : 84.95 % Rotamer: Outliers : 0.37 % Allowed : 3.58 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.30 % 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: -4.74 (0.11), residues: 3807 helix: -2.38 (0.10), residues: 1489 sheet: -3.60 (0.20), residues: 397 loop : -3.76 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP I 807 HIS 0.017 0.003 HIS I 673 PHE 0.033 0.004 PHE H 231 TYR 0.040 0.004 TYR I1229 ARG 0.014 0.002 ARG J 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 776 time to evaluate : 3.623 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 outliers start: 12 outliers final: 2 residues processed: 785 average time/residue: 0.5108 time to fit residues: 603.2374 Evaluate side-chains 417 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 415 time to evaluate : 3.681 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2749 time to fit residues: 6.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 320 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 297 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 344 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 37 HIS I 69 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 343 HIS I 510 GLN I 513 GLN I 573 ASN I 580 GLN I 628 HIS ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1017 GLN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS I1264 GLN J 435 GLN J 465 GLN J 680 ASN J 720 ASN J1197 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN J1295 ASN J1366 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN L 317 ASN L 383 ASN L 446 GLN L 518 HIS L 600 HIS M 21 ASN M 68 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30634 Z= 0.210 Angle : 0.704 9.874 41383 Z= 0.359 Chirality : 0.045 0.184 4744 Planarity : 0.005 0.090 5404 Dihedral : 6.430 114.431 4488 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer: Outliers : 2.21 % Allowed : 9.93 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.12), residues: 3807 helix: -0.71 (0.12), residues: 1505 sheet: -2.96 (0.22), residues: 402 loop : -3.04 (0.12), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 807 HIS 0.021 0.001 HIS I 165 PHE 0.018 0.002 PHE I 136 TYR 0.023 0.002 TYR G 185 ARG 0.008 0.001 ARG I1223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 563 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 28 residues processed: 609 average time/residue: 0.4601 time to fit residues: 442.3182 Evaluate side-chains 421 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 393 time to evaluate : 3.513 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2860 time to fit residues: 20.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 286 optimal weight: 0.3980 chunk 234 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 341 optimal weight: 8.9990 chunk 117 optimal weight: 0.0060 chunk 276 optimal weight: 30.0000 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN I 618 GLN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1136 GLN I1157 GLN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 GLN L 568 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30634 Z= 0.261 Angle : 0.670 12.918 41383 Z= 0.340 Chirality : 0.044 0.197 4744 Planarity : 0.005 0.089 5404 Dihedral : 6.008 95.456 4488 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.51 % Favored : 91.31 % Rotamer: Outliers : 2.70 % Allowed : 13.24 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.13), residues: 3807 helix: -0.24 (0.13), residues: 1517 sheet: -2.58 (0.23), residues: 398 loop : -2.77 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 807 HIS 0.014 0.001 HIS I 165 PHE 0.016 0.002 PHE L 610 TYR 0.035 0.002 TYR H 177 ARG 0.005 0.000 ARG J 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 413 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 36 residues processed: 477 average time/residue: 0.4513 time to fit residues: 341.4888 Evaluate side-chains 383 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 347 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3563 time to fit residues: 28.6873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 340 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 346 optimal weight: 0.0270 chunk 366 optimal weight: 0.0980 chunk 180 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN J 157 GLN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J1289 ASN J1295 ASN L 30 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN L 317 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30634 Z= 0.187 Angle : 0.616 10.096 41383 Z= 0.309 Chirality : 0.043 0.464 4744 Planarity : 0.004 0.085 5404 Dihedral : 5.547 78.158 4488 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.70 % Rotamer: Outliers : 2.14 % Allowed : 14.89 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.11 % 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 (0.13), residues: 3807 helix: 0.19 (0.13), residues: 1522 sheet: -2.31 (0.24), residues: 386 loop : -2.55 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 807 HIS 0.006 0.001 HIS I1070 PHE 0.012 0.001 PHE I 136 TYR 0.026 0.001 TYR H 177 ARG 0.006 0.000 ARG J 610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 440 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 26 residues processed: 489 average time/residue: 0.4273 time to fit residues: 336.6650 Evaluate side-chains 385 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 359 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2927 time to fit residues: 18.8063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 305 optimal weight: 0.1980 chunk 207 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 510 GLN I 894 GLN I1157 GLN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN J1295 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4182 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: