Starting phenix.real_space_refine on Tue Nov 21 03:00:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2i_27837/11_2023/8e2i_27837_trim.pdb" } resolution = 3.04 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= -0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 310 5.16 5 C 29470 2.51 5 N 7864 2.21 5 O 8530 1.98 5 H 46502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 92676 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 43333 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2745, 43158 Classifications: {'peptide': 2745} Link IDs: {'PTRANS': 132, 'TRANS': 2612} Chain breaks: 48 Conformer: "B" Number of residues, atoms: 2745, 43158 Classifications: {'peptide': 2745} Link IDs: {'PTRANS': 132, 'TRANS': 2612} Chain breaks: 48 bond proxies already assigned to first conformer: 43367 Chain: "B" Number of atoms: 43331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2745, 43156 Classifications: {'peptide': 2745} Link IDs: {'PTRANS': 132, 'TRANS': 2612} Chain breaks: 48 Conformer: "B" Number of residues, atoms: 2745, 43156 Classifications: {'peptide': 2745} Link IDs: {'PTRANS': 132, 'TRANS': 2612} Chain breaks: 48 bond proxies already assigned to first conformer: 43365 Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N ACYS A2642 " occ=0.10 ... (20 atoms not shown) pdb=" HG BCYS A2642 " occ=0.10 residue: pdb=" N ASER A2703 " occ=0.28 ... (20 atoms not shown) pdb=" HG BSER A2703 " occ=0.72 residue: pdb=" N ASER A2725 " occ=0.04 ... (20 atoms not shown) pdb=" HG BSER A2725 " occ=0.96 residue: pdb=" N AVAL A2753 " occ=0.08 ... (30 atoms not shown) pdb="HG23BVAL A2753 " occ=0.08 residue: pdb=" N ASER A2809 " occ=0.24 ... (20 atoms not shown) pdb=" HG BSER A2809 " occ=0.24 residue: pdb=" N ATHR A3074 " occ=0.28 ... (26 atoms not shown) pdb="HG23BTHR A3074 " occ=0.72 residue: pdb=" N AILE A3118 " occ=0.00 ... (36 atoms not shown) pdb="HD13BILE A3118 " occ=0.00 residue: pdb=" N AVAL A3257 " occ=0.48 ... (30 atoms not shown) pdb="HG23BVAL A3257 " occ=0.48 residue: pdb=" N ASER A3368 " occ=0.31 ... (20 atoms not shown) pdb=" HG BSER A3368 " occ=0.69 residue: pdb=" N AILE A3392 " occ=0.34 ... (36 atoms not shown) pdb="HD13BILE A3392 " occ=0.34 residue: pdb=" N ACYS B2642 " occ=0.06 ... (20 atoms not shown) pdb=" HG BCYS B2642 " occ=0.06 residue: pdb=" N ASER B2703 " occ=0.18 ... (20 atoms not shown) pdb=" HG BSER B2703 " occ=0.82 ... (remaining 9 not shown) Time building chain proxies: 53.29, per 1000 atoms: 0.58 Number of scatterers: 92676 At special positions: 0 Unit cell: (172.728, 211.112, 191.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 310 16.00 O 8530 8.00 N 7864 7.00 C 29470 6.00 H 46502 1.00 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=0, symmetry=0 Time building additional restraints: 61.88 Conformation dependent library (CDL) restraints added in 12.7 seconds 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11412 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 35 sheets defined 60.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.567A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.706A pdb=" N GLN A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 4.181A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1029 Processing helix chain 'A' and resid 1050 through 1055 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.529A pdb=" N GLN A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1073 removed outlier: 3.555A pdb=" N GLN A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1177 Processing helix chain 'A' and resid 1189 through 1192 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1291 through 1296 Processing helix chain 'A' and resid 1313 through 1324 Processing helix chain 'A' and resid 1324 through 1336 removed outlier: 4.179A pdb=" N HIS A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 Processing helix chain 'A' and resid 1345 through 1364 Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1384 through 1395 Processing helix chain 'A' and resid 1397 through 1414 Processing helix chain 'A' and resid 1423 through 1437 removed outlier: 4.097A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1442 Processing helix chain 'A' and resid 1444 through 1459 removed outlier: 3.542A pdb=" N TRP A1450 " --> pdb=" O GLY A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1484 removed outlier: 3.820A pdb=" N GLN A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1497 Processing helix chain 'A' and resid 1559 through 1563 removed outlier: 3.599A pdb=" N GLU A1562 " --> pdb=" O GLY A1559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1563 " --> pdb=" O LEU A1560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1559 through 1563' Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1885 through 1890 Processing helix chain 'A' and resid 1912 through 1941 removed outlier: 3.948A pdb=" N SER A1941 " --> pdb=" O THR A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1960 through 1998 Processing helix chain 'A' and resid 2012 through 2018 Processing helix chain 'A' and resid 2019 through 2040 Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2091 through 2105 Processing helix chain 'A' and resid 2113 through 2128 Processing helix chain 'A' and resid 2132 through 2147 Processing helix chain 'A' and resid 2164 through 2182 Processing helix chain 'A' and resid 2326 through 2342 Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.678A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A2365 " --> pdb=" O ILE A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2375 Processing helix chain 'A' and resid 2376 through 2389 removed outlier: 3.764A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2400 through 2420 Processing helix chain 'A' and resid 2568 through 2573 Processing helix chain 'A' and resid 2576 through 2599 Processing helix chain 'A' and resid 2635 through 2649 Processing helix chain 'A' and resid 2656 through 2669 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2731 removed outlier: 3.705A pdb=" N ASN A2731 " --> pdb=" O THR A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2747 through 2755 Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.004A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2781 through 2802 removed outlier: 4.215A pdb=" N ALA A2785 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 4.194A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2844 Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2915 through 2931 removed outlier: 3.604A pdb=" N GLN A2931 " --> pdb=" O ASN A2927 " (cutoff:3.500A) Processing helix chain 'A' and resid 2980 through 2987 Processing helix chain 'A' and resid 2987 through 3000 Processing helix chain 'A' and resid 3031 through 3047 Processing helix chain 'A' and resid 3049 through 3062 removed outlier: 3.527A pdb=" N MET A3053 " --> pdb=" O THR A3049 " (cutoff:3.500A) Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3064 through 3068 Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3102 through 3117 Processing helix chain 'A' and resid 3124 through 3133 Processing helix chain 'A' and resid 3164 through 3167 Processing helix chain 'A' and resid 3179 through 3184 removed outlier: 3.783A pdb=" N LEU A3183 " --> pdb=" O ALA A3179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A3184 " --> pdb=" O GLU A3180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3179 through 3184' Processing helix chain 'A' and resid 3231 through 3235 Processing helix chain 'A' and resid 3305 through 3309 removed outlier: 3.734A pdb=" N SER A3309 " --> pdb=" O THR A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3326 Processing helix chain 'A' and resid 3327 through 3340 removed outlier: 3.636A pdb=" N LEU A3331 " --> pdb=" O SER A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3341 through 3353 removed outlier: 4.532A pdb=" N GLY A3346 " --> pdb=" O SER A3342 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N MET A3347 " --> pdb=" O ASP A3343 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3374 through 3388 removed outlier: 3.556A pdb=" N ILE A3378 " --> pdb=" O HIS A3374 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3428 through 3441 Processing helix chain 'A' and resid 3445 through 3466 Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3490 through 3508 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.662A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3532 Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3564 removed outlier: 4.031A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A3558 " --> pdb=" O PRO A3554 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3617 Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3630 through 3645 Processing helix chain 'A' and resid 3679 through 3695 removed outlier: 3.599A pdb=" N VAL A3683 " --> pdb=" O THR A3679 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A3684 " --> pdb=" O ALA A3680 " (cutoff:3.500A) Proline residue: A3685 - end of helix Processing helix chain 'A' and resid 3696 through 3704 Processing helix chain 'A' and resid 3708 through 3720 removed outlier: 3.760A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A3713 " --> pdb=" O ASN A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 Processing helix chain 'A' and resid 3774 through 3790 Processing helix chain 'A' and resid 3806 through 3816 Processing helix chain 'A' and resid 3846 through 3850 Processing helix chain 'A' and resid 3865 through 3872 Processing helix chain 'A' and resid 3982 through 3993 Processing helix chain 'A' and resid 4069 through 4077 Processing helix chain 'A' and resid 4078 through 4085 removed outlier: 3.871A pdb=" N LEU A4082 " --> pdb=" O GLY A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4165 Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4177 through 4189 Processing helix chain 'A' and resid 4199 through 4203 Processing helix chain 'A' and resid 4205 through 4209 removed outlier: 3.657A pdb=" N VAL A4208 " --> pdb=" O SER A4205 " (cutoff:3.500A) Processing helix chain 'A' and resid 4211 through 4223 Processing helix chain 'A' and resid 4228 through 4242 removed outlier: 3.632A pdb=" N VAL A4232 " --> pdb=" O THR A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4242 through 4256 Processing helix chain 'A' and resid 4306 through 4332 Processing helix chain 'A' and resid 4358 through 4367 removed outlier: 4.474A pdb=" N GLU A4362 " --> pdb=" O SER A4358 " (cutoff:3.500A) Processing helix chain 'A' and resid 4368 through 4378 Processing helix chain 'A' and resid 4381 through 4387 removed outlier: 3.575A pdb=" N ARG A4387 " --> pdb=" O LEU A4383 " (cutoff:3.500A) Processing helix chain 'A' and resid 4388 through 4404 Processing helix chain 'A' and resid 4408 through 4412 Processing helix chain 'A' and resid 4432 through 4455 Processing helix chain 'A' and resid 4477 through 4499 removed outlier: 4.160A pdb=" N GLN A4482 " --> pdb=" O VAL A4478 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 225 through 243 Processing helix chain 'B' and resid 247 through 263 removed outlier: 3.560A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.073A pdb=" N TYR B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.544A pdb=" N PHE B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.545A pdb=" N THR B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.721A pdb=" N MET B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.583A pdb=" N GLN B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 removed outlier: 4.125A pdb=" N GLU B 728 " --> pdb=" O LYS B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1030 Processing helix chain 'B' and resid 1050 through 1055 Processing helix chain 'B' and resid 1060 through 1065 removed outlier: 3.930A pdb=" N GLN B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1073 removed outlier: 3.983A pdb=" N HIS B1073 " --> pdb=" O ASP B1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1069 through 1073' Processing helix chain 'B' and resid 1171 through 1177 Processing helix chain 'B' and resid 1189 through 1192 Processing helix chain 'B' and resid 1205 through 1210 Processing helix chain 'B' and resid 1291 through 1296 Processing helix chain 'B' and resid 1313 through 1324 Processing helix chain 'B' and resid 1324 through 1336 removed outlier: 3.719A pdb=" N HIS B1328 " --> pdb=" O PHE B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1343 Processing helix chain 'B' and resid 1345 through 1364 Processing helix chain 'B' and resid 1377 through 1384 Processing helix chain 'B' and resid 1384 through 1395 Processing helix chain 'B' and resid 1397 through 1414 removed outlier: 3.566A pdb=" N ASN B1414 " --> pdb=" O LEU B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1437 removed outlier: 4.222A pdb=" N VAL B1427 " --> pdb=" O ALA B1423 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B1437 " --> pdb=" O LEU B1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1442 Processing helix chain 'B' and resid 1444 through 1459 Processing helix chain 'B' and resid 1462 through 1484 Processing helix chain 'B' and resid 1486 through 1497 Processing helix chain 'B' and resid 1823 through 1828 Processing helix chain 'B' and resid 1885 through 1890 Processing helix chain 'B' and resid 1912 through 1941 removed outlier: 3.914A pdb=" N SER B1941 " --> pdb=" O THR B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1949 through 1958 Processing helix chain 'B' and resid 1960 through 1998 Processing helix chain 'B' and resid 2012 through 2018 Processing helix chain 'B' and resid 2019 through 2040 Processing helix chain 'B' and resid 2055 through 2067 Processing helix chain 'B' and resid 2071 through 2087 Processing helix chain 'B' and resid 2091 through 2105 Processing helix chain 'B' and resid 2113 through 2128 Processing helix chain 'B' and resid 2131 through 2147 removed outlier: 4.262A pdb=" N LEU B2135 " --> pdb=" O ASN B2131 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2150 No H-bonds generated for 'chain 'B' and resid 2148 through 2150' Processing helix chain 'B' and resid 2164 through 2182 Processing helix chain 'B' and resid 2326 through 2342 Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.589A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B2365 " --> pdb=" O ILE B2361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2370 through 2375 Processing helix chain 'B' and resid 2376 through 2389 removed outlier: 3.663A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 3.614A pdb=" N GLU B2572 " --> pdb=" O ALA B2569 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B2573 " --> pdb=" O ARG B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2599 Processing helix chain 'B' and resid 2635 through 2649 Processing helix chain 'B' and resid 2656 through 2669 Processing helix chain 'B' and resid 2697 through 2711 Processing helix chain 'B' and resid 2715 through 2731 Processing helix chain 'B' and resid 2747 through 2755 Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.019A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2781 through 2802 removed outlier: 4.198A pdb=" N ALA B2785 " --> pdb=" O VAL B2781 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2821 removed outlier: 4.067A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2845 removed outlier: 3.750A pdb=" N GLU B2845 " --> pdb=" O GLU B2841 " (cutoff:3.500A) Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2915 through 2931 removed outlier: 3.688A pdb=" N GLN B2931 " --> pdb=" O ASN B2927 " (cutoff:3.500A) Processing helix chain 'B' and resid 2980 through 2987 Processing helix chain 'B' and resid 2987 through 3000 Processing helix chain 'B' and resid 3031 through 3047 Processing helix chain 'B' and resid 3049 through 3062 removed outlier: 3.525A pdb=" N MET B3053 " --> pdb=" O THR B3049 " (cutoff:3.500A) Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3064 through 3068 Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3102 through 3118 Processing helix chain 'B' and resid 3124 through 3133 Processing helix chain 'B' and resid 3164 through 3167 Processing helix chain 'B' and resid 3179 through 3184 removed outlier: 3.895A pdb=" N LEU B3183 " --> pdb=" O ALA B3179 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B3184 " --> pdb=" O GLU B3180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3179 through 3184' Processing helix chain 'B' and resid 3231 through 3235 Processing helix chain 'B' and resid 3305 through 3309 removed outlier: 3.920A pdb=" N SER B3309 " --> pdb=" O THR B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3326 Processing helix chain 'B' and resid 3327 through 3341 removed outlier: 3.798A pdb=" N LEU B3331 " --> pdb=" O SER B3327 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE B3341 " --> pdb=" O CYS B3337 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3353 Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3374 through 3387 removed outlier: 3.638A pdb=" N ILE B3378 " --> pdb=" O HIS B3374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3402 Processing helix chain 'B' and resid 3428 through 3441 Processing helix chain 'B' and resid 3445 through 3466 Processing helix chain 'B' and resid 3484 through 3488 Processing helix chain 'B' and resid 3490 through 3508 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.701A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B3517 " --> pdb=" O LEU B3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3512 through 3517' Processing helix chain 'B' and resid 3518 through 3532 Processing helix chain 'B' and resid 3536 through 3553 Processing helix chain 'B' and resid 3553 through 3565 removed outlier: 3.763A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B3558 " --> pdb=" O PRO B3554 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3617 Processing helix chain 'B' and resid 3619 through 3629 Processing helix chain 'B' and resid 3630 through 3645 Processing helix chain 'B' and resid 3679 through 3695 removed outlier: 4.261A pdb=" N ALA B3684 " --> pdb=" O ALA B3680 " (cutoff:3.500A) Proline residue: B3685 - end of helix Processing helix chain 'B' and resid 3696 through 3704 Processing helix chain 'B' and resid 3708 through 3720 removed outlier: 3.640A pdb=" N TRP B3712 " --> pdb=" O VAL B3708 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B3713 " --> pdb=" O ASN B3709 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 Processing helix chain 'B' and resid 3774 through 3790 Processing helix chain 'B' and resid 3806 through 3816 removed outlier: 3.501A pdb=" N ARG B3810 " --> pdb=" O GLY B3806 " (cutoff:3.500A) Processing helix chain 'B' and resid 3846 through 3850 Processing helix chain 'B' and resid 3865 through 3872 Processing helix chain 'B' and resid 3981 through 3993 removed outlier: 4.205A pdb=" N GLN B3985 " --> pdb=" O MET B3981 " (cutoff:3.500A) Processing helix chain 'B' and resid 4069 through 4077 Processing helix chain 'B' and resid 4078 through 4085 removed outlier: 3.533A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B4085 " --> pdb=" O ALA B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4165 Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4177 through 4189 Processing helix chain 'B' and resid 4199 through 4203 Processing helix chain 'B' and resid 4205 through 4209 removed outlier: 3.712A pdb=" N VAL B4208 " --> pdb=" O SER B4205 " (cutoff:3.500A) Processing helix chain 'B' and resid 4211 through 4223 Processing helix chain 'B' and resid 4228 through 4242 removed outlier: 3.767A pdb=" N VAL B4232 " --> pdb=" O THR B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4242 through 4256 Processing helix chain 'B' and resid 4306 through 4332 Processing helix chain 'B' and resid 4359 through 4367 Processing helix chain 'B' and resid 4368 through 4378 Processing helix chain 'B' and resid 4381 through 4388 removed outlier: 3.684A pdb=" N HIS B4388 " --> pdb=" O ASP B4384 " (cutoff:3.500A) Processing helix chain 'B' and resid 4388 through 4404 Processing helix chain 'B' and resid 4408 through 4412 Processing helix chain 'B' and resid 4432 through 4455 Processing helix chain 'B' and resid 4477 through 4499 removed outlier: 3.920A pdb=" N GLN B4482 " --> pdb=" O VAL B4478 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 65 Processing helix chain 'F' and resid 70 through 120 removed outlier: 4.431A pdb=" N GLU F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 181 Processing helix chain 'E' and resid 13 through 65 Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 70 through 120 removed outlier: 5.041A pdb=" N GLU E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 181 Processing helix chain 'C' and resid 52 through 107 Processing helix chain 'D' and resid 52 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.080A pdb=" N ALA A 81 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 91 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A 104 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 93 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.329A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 409 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 423 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 411 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 419 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 513 removed outlier: 6.217A pdb=" N GLY A 570 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 510 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 568 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 512 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N CYS A 566 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 571 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 629 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER A 634 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 716 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 731 through 738 removed outlier: 6.821A pdb=" N GLY A 748 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 736 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 746 " --> pdb=" O ILE A 736 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 902 through 903 removed outlier: 6.068A pdb=" N VAL A 912 " --> pdb=" O LYS A 925 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 925 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 914 " --> pdb=" O LEU A 923 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 940 through 945 Processing sheet with id=AB1, first strand: chain 'A' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1031 through 1033 current: chain 'A' and resid 1075 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1075 through 1079 current: chain 'A' and resid 1200 through 1203 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 6.243A pdb=" N ILE A1120 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A1186 " --> pdb=" O ILE A1120 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL A1122 " --> pdb=" O GLY A1184 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLY A1184 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A1124 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1564 through 1565 removed outlier: 6.541A pdb=" N HIS A1881 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU A1801 " --> pdb=" O HIS A1881 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1569 through 1573 removed outlier: 5.694A pdb=" N CYS A1570 " --> pdb=" O ASP A1794 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP A1794 " --> pdb=" O CYS A1570 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A1572 " --> pdb=" O THR A1792 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A1855 " --> pdb=" O ILE A1819 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A1819 " --> pdb=" O PHE A1855 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A1857 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A1817 " --> pdb=" O LYS A1857 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1859 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A1815 " --> pdb=" O THR A1859 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A1861 " --> pdb=" O ALA A1813 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A1815 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A1833 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A1817 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1578 through 1580 removed outlier: 3.554A pdb=" N GLU A1580 " --> pdb=" O SER A1777 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A1777 " --> pdb=" O GLU A1580 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2877 through 2878 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2878 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 2941 through 2943 removed outlier: 5.388A pdb=" N ALA A2978 " --> pdb=" O LEU A2934 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3855 through 3861 removed outlier: 9.520A pdb=" N ILE A4002 " --> pdb=" O LYS A3821 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A3823 " --> pdb=" O ILE A4002 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU A4004 " --> pdb=" O THR A3823 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A3825 " --> pdb=" O LEU A4004 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A4006 " --> pdb=" O PHE A3825 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A3827 " --> pdb=" O VAL A4006 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.216A pdb=" N ALA B 81 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP B 95 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B 101 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AC2, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 166 Processing sheet with id=AC4, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AC5, first strand: chain 'B' and resid 388 through 390 removed outlier: 6.395A pdb=" N ALA B 403 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 409 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 423 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 411 " --> pdb=" O HIS B 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 504 through 513 removed outlier: 6.156A pdb=" N GLY B 570 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 510 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 568 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 512 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 566 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER B 634 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 716 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 731 through 738 removed outlier: 6.796A pdb=" N GLY B 748 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 736 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 746 " --> pdb=" O ILE B 736 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 902 through 903 removed outlier: 6.063A pdb=" N VAL B 912 " --> pdb=" O LYS B 925 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 925 " --> pdb=" O VAL B 912 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE B 914 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 940 through 945 removed outlier: 3.826A pdb=" N SER B 942 " --> pdb=" O CYS B 955 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1031 through 1033 current: chain 'B' and resid 1074 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1074 through 1079 current: chain 'B' and resid 1199 through 1203 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 6.752A pdb=" N ILE B1120 " --> pdb=" O VAL B1186 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B1186 " --> pdb=" O ILE B1120 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B1122 " --> pdb=" O GLY B1184 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B1184 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B1124 " --> pdb=" O LEU B1182 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1564 through 1565 removed outlier: 6.436A pdb=" N HIS B1881 " --> pdb=" O LEU B1801 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU B1801 " --> pdb=" O HIS B1881 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B1804 " --> pdb=" O LEU B1844 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1569 through 1573 removed outlier: 7.106A pdb=" N THR B1792 " --> pdb=" O VAL B1571 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR B1573 " --> pdb=" O PHE B1790 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B1790 " --> pdb=" O THR B1573 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B1814 " --> pdb=" O ILE B1861 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B1815 " --> pdb=" O VAL B1833 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1833 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B1817 " --> pdb=" O LEU B1831 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1578 through 1580 Processing sheet with id=AD6, first strand: chain 'B' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2879 current: chain 'B' and resid 3251 through 3252 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 2941 through 2943 removed outlier: 5.287A pdb=" N ALA B2978 " --> pdb=" O LEU B2934 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 3855 through 3861 removed outlier: 9.154A pdb=" N ILE B4002 " --> pdb=" O LYS B3821 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR B3823 " --> pdb=" O ILE B4002 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU B4004 " --> pdb=" O THR B3823 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE B3825 " --> pdb=" O LEU B4004 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B4006 " --> pdb=" O PHE B3825 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN B3827 " --> pdb=" O VAL B4006 " (cutoff:3.500A) 2733 hydrogen bonds defined for protein. 7934 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: 41.34 Time building geometry restraints manager: 64.87 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: 46336 1.03 - 1.23: 232 1.23 - 1.42: 18737 1.42 - 1.62: 27761 1.62 - 1.82: 454 Bond restraints: 93520 Sorted by residual: bond pdb=" C LEU A1485 " pdb=" N THR A1486 " ideal model delta sigma weight residual 1.339 1.256 0.084 5.57e-02 3.22e+02 2.27e+00 bond pdb=" CB VAL E 26 " pdb=" CG2 VAL E 26 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU B1353 " pdb=" CD1 LEU B1353 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL F 23 " pdb=" CG2 VAL F 23 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.61e-01 bond pdb=" CB VAL B2083 " pdb=" CG2 VAL B2083 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.75e-01 ... (remaining 93515 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.40: 1435 106.40 - 113.36: 113771 113.36 - 120.31: 28188 120.31 - 127.27: 25393 127.27 - 134.22: 600 Bond angle restraints: 169387 Sorted by residual: angle pdb=" C VAL B4409 " pdb=" CA VAL B4409 " pdb=" CB VAL B4409 " ideal model delta sigma weight residual 113.70 110.35 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" CA TYR F 117 " pdb=" CB TYR F 117 " pdb=" CG TYR F 117 " ideal model delta sigma weight residual 113.90 108.75 5.15 1.80e+00 3.09e-01 8.17e+00 angle pdb=" CA GLU E 114 " pdb=" CB GLU E 114 " pdb=" CG GLU E 114 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" CA TYR F 95 " pdb=" CB TYR F 95 " pdb=" CG TYR F 95 " ideal model delta sigma weight residual 113.90 118.75 -4.85 1.80e+00 3.09e-01 7.27e+00 angle pdb=" N CYS A 117 " pdb=" CA CYS A 117 " pdb=" C CYS A 117 " ideal model delta sigma weight residual 113.19 109.26 3.93 1.58e+00 4.01e-01 6.18e+00 ... (remaining 169382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 34172 17.79 - 35.58: 2561 35.58 - 53.37: 643 53.37 - 71.16: 162 71.16 - 88.95: 63 Dihedral angle restraints: 37601 sinusoidal: 17667 harmonic: 19934 Sorted by residual: dihedral pdb=" CA LYS B 416 " pdb=" C LYS B 416 " pdb=" N LEU B 417 " pdb=" CA LEU B 417 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS A 416 " pdb=" C LYS A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta harmonic sigma weight residual 180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A3999 " pdb=" C TYR A3999 " pdb=" N ARG A4000 " pdb=" CA ARG A4000 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 37598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5069 0.031 - 0.062: 1789 0.062 - 0.093: 581 0.093 - 0.124: 256 0.124 - 0.155: 49 Chirality restraints: 7744 Sorted by residual: chirality pdb=" CA ILE A 82 " pdb=" N ILE A 82 " pdb=" C ILE A 82 " pdb=" CB ILE A 82 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE A 914 " pdb=" N ILE A 914 " pdb=" C ILE A 914 " pdb=" CB ILE A 914 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE A3296 " pdb=" N ILE A3296 " pdb=" C ILE A3296 " pdb=" CB ILE A3296 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 7741 not shown) Planarity restraints: 13522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1390 " 0.229 9.50e-02 1.11e+02 7.67e-02 7.63e+00 pdb=" NE ARG A1390 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A1390 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A1390 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A1390 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A1390 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A1390 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1390 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1390 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 165 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C THR E 165 " -0.039 2.00e-02 2.50e+03 pdb=" O THR E 165 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN E 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 78 " -0.007 2.00e-02 2.50e+03 1.05e-02 4.45e+00 pdb=" CG TRP E 78 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP E 78 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 78 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 78 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP E 78 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP E 78 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 78 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 78 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 78 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP E 78 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP E 78 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP E 78 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 78 " 0.011 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 78 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP E 78 " 0.017 2.00e-02 2.50e+03 ... (remaining 13519 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1932 2.08 - 2.71: 159695 2.71 - 3.34: 286426 3.34 - 3.97: 359816 3.97 - 4.60: 570246 Nonbonded interactions: 1378115 Sorted by model distance: nonbonded pdb=" O GLN B3827 " pdb=" H VAL B4006 " model vdw 1.453 1.850 nonbonded pdb=" O ASP A 131 " pdb=" H ILE A 388 " model vdw 1.477 1.850 nonbonded pdb=" H LYS A 156 " pdb=" OD2 ASP A 159 " model vdw 1.487 1.850 nonbonded pdb=" OD1 ASN A3249 " pdb=" H TYR B2686 " model vdw 1.500 1.850 nonbonded pdb=" O VAL A3258 " pdb="HH12 ARG B3286 " model vdw 1.500 1.850 ... (remaining 1378110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 2641 or resid 2644 through 2702 or resid 2705 t \ hrough 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 2755 \ through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 3076 \ through 3117 or resid 3120 through 3192 or (resid 3193 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or na \ me HG3 or name HD2 or name HD3 or name HE )) or resid 3194 through 3256 or resid \ 3259 through 3367 or resid 3369 through 3391 or resid 3394 through 4499)) selection = (chain 'B' and (resid 68 through 2641 or resid 2644 through 2702 or resid 2705 t \ hrough 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 2755 \ through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 3076 \ through 3117 or resid 3120 through 3256 or resid 3259 through 3367 or resid 336 \ 9 through 3391 or resid 3394 through 4499)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.110 Extract box with map and model: 12.540 Check model and map are aligned: 1.050 Set scattering table: 0.680 Process input model: 268.820 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.480 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: 0.020 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 292.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 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 : 0.004 0.084 47018 Z= 0.261 Angle : 0.599 6.878 63872 Z= 0.317 Chirality : 0.039 0.155 7744 Planarity : 0.005 0.102 7996 Dihedral : 15.469 88.947 17070 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.83 % Allowed : 15.98 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 5708 helix: 1.75 (0.09), residues: 3138 sheet: -0.32 (0.21), residues: 603 loop : -0.27 (0.14), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 906 time to evaluate : 6.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 39 outliers final: 8 residues processed: 935 average time/residue: 1.2288 time to fit residues: 1861.1088 Evaluate side-chains 534 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 526 time to evaluate : 5.450 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.1357 time to fit residues: 21.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 499 optimal weight: 8.9990 chunk 448 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 464 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 537 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 311 GLN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2670 ASN A2868 HIS A2931 GLN A3283 HIS A3322 GLN ** A3377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3495 HIS B 244 GLN B 317 GLN B 718 GLN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 HIS B1951 ASN ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 ASN ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2989 GLN B3495 HIS F 143 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 47018 Z= 0.355 Angle : 0.661 7.415 63872 Z= 0.348 Chirality : 0.041 0.174 7744 Planarity : 0.005 0.070 7996 Dihedral : 4.231 20.152 6278 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 5708 helix: 1.35 (0.09), residues: 3161 sheet: -0.37 (0.21), residues: 612 loop : -0.40 (0.14), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 527 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 101 outliers final: 56 residues processed: 608 average time/residue: 1.1509 time to fit residues: 1161.1105 Evaluate side-chains 519 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 463 time to evaluate : 5.470 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 3 residues processed: 56 average time/residue: 0.9050 time to fit residues: 99.5505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 447 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 538 optimal weight: 9.9990 chunk 581 optimal weight: 20.0000 chunk 479 optimal weight: 2.9990 chunk 534 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 432 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1055 GLN ** A1456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3527 ASN ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN E 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47018 Z= 0.239 Angle : 0.568 7.874 63872 Z= 0.294 Chirality : 0.038 0.212 7744 Planarity : 0.004 0.070 7996 Dihedral : 4.089 21.976 6278 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.03 % Allowed : 16.62 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5708 helix: 1.57 (0.09), residues: 3163 sheet: -0.37 (0.21), residues: 611 loop : -0.34 (0.15), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 498 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 48 outliers final: 28 residues processed: 532 average time/residue: 1.1465 time to fit residues: 1026.1270 Evaluate side-chains 480 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 452 time to evaluate : 5.398 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.8522 time to fit residues: 51.8619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 532 optimal weight: 9.9990 chunk 404 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 361 optimal weight: 6.9990 chunk 540 optimal weight: 3.9990 chunk 572 optimal weight: 7.9990 chunk 282 optimal weight: 0.0010 chunk 512 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3377 ASN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 47018 Z= 0.184 Angle : 0.537 7.756 63872 Z= 0.273 Chirality : 0.037 0.164 7744 Planarity : 0.004 0.056 7996 Dihedral : 3.939 20.404 6278 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.60 % Allowed : 16.76 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 5708 helix: 1.80 (0.09), residues: 3174 sheet: -0.33 (0.21), residues: 632 loop : -0.25 (0.15), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 489 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 25 outliers final: 14 residues processed: 505 average time/residue: 1.1377 time to fit residues: 961.7913 Evaluate side-chains 461 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 447 time to evaluate : 5.429 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.8627 time to fit residues: 29.4434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 476 optimal weight: 8.9990 chunk 324 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 426 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 488 optimal weight: 3.9990 chunk 395 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 292 optimal weight: 0.6980 chunk 513 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 47018 Z= 0.266 Angle : 0.571 9.351 63872 Z= 0.295 Chirality : 0.038 0.154 7744 Planarity : 0.004 0.056 7996 Dihedral : 4.053 19.911 6278 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.77 % Allowed : 17.03 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 5708 helix: 1.64 (0.09), residues: 3164 sheet: -0.42 (0.21), residues: 629 loop : -0.43 (0.15), residues: 1915 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 455 time to evaluate : 5.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 34 outliers final: 20 residues processed: 480 average time/residue: 1.1650 time to fit residues: 939.9008 Evaluate side-chains 454 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 434 time to evaluate : 5.364 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.8936 time to fit residues: 40.1940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 192 optimal weight: 2.9990 chunk 515 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 572 optimal weight: 8.9990 chunk 475 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 300 optimal weight: 0.0770 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2760 HIS ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3051 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 47018 Z= 0.276 Angle : 0.574 7.997 63872 Z= 0.298 Chirality : 0.038 0.152 7744 Planarity : 0.004 0.055 7996 Dihedral : 4.137 19.620 6278 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.81 % Allowed : 16.99 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 5708 helix: 1.54 (0.09), residues: 3165 sheet: -0.56 (0.20), residues: 652 loop : -0.55 (0.15), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 459 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 36 outliers final: 19 residues processed: 482 average time/residue: 1.1846 time to fit residues: 961.4785 Evaluate side-chains 446 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 427 time to evaluate : 5.495 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.9480 time to fit residues: 39.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 552 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 418 optimal weight: 0.3980 chunk 324 optimal weight: 20.0000 chunk 482 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 570 optimal weight: 6.9990 chunk 357 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3109 ASN A3609 HIS ** A4180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3109 ASN B3336 HIS ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 47018 Z= 0.330 Angle : 0.618 8.094 63872 Z= 0.323 Chirality : 0.040 0.177 7744 Planarity : 0.005 0.055 7996 Dihedral : 4.323 19.473 6278 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.72 % Allowed : 17.28 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5708 helix: 1.25 (0.09), residues: 3167 sheet: -0.63 (0.20), residues: 645 loop : -0.75 (0.15), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 449 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 31 outliers final: 16 residues processed: 468 average time/residue: 1.1440 time to fit residues: 899.0796 Evaluate side-chains 443 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 427 time to evaluate : 5.417 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.9379 time to fit residues: 34.1413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 353 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 362 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 448 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 47018 Z= 0.268 Angle : 0.577 8.047 63872 Z= 0.299 Chirality : 0.038 0.192 7744 Planarity : 0.004 0.054 7996 Dihedral : 4.242 19.399 6278 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.35 % Allowed : 17.63 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5708 helix: 1.39 (0.09), residues: 3161 sheet: -0.68 (0.20), residues: 655 loop : -0.70 (0.15), residues: 1892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 438 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 445 average time/residue: 1.1540 time to fit residues: 863.1250 Evaluate side-chains 432 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 424 time to evaluate : 5.545 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.8626 time to fit residues: 20.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 519 optimal weight: 6.9990 chunk 546 optimal weight: 4.9990 chunk 498 optimal weight: 0.7980 chunk 531 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 417 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 480 optimal weight: 2.9990 chunk 502 optimal weight: 0.8980 chunk 529 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 HIS B1055 GLN ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3283 HIS ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47018 Z= 0.173 Angle : 0.531 7.903 63872 Z= 0.269 Chirality : 0.037 0.181 7744 Planarity : 0.004 0.051 7996 Dihedral : 3.999 19.128 6278 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.25 % Allowed : 17.67 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5708 helix: 1.78 (0.09), residues: 3167 sheet: -0.47 (0.20), residues: 636 loop : -0.51 (0.15), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 450 time to evaluate : 5.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 452 average time/residue: 1.1903 time to fit residues: 915.5985 Evaluate side-chains 432 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 426 time to evaluate : 5.485 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.9755 time to fit residues: 17.6148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 349 optimal weight: 6.9990 chunk 562 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 chunk 589 optimal weight: 20.0000 chunk 542 optimal weight: 2.9990 chunk 469 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2016 GLN ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 47018 Z= 0.371 Angle : 0.629 8.078 63872 Z= 0.332 Chirality : 0.041 0.202 7744 Planarity : 0.005 0.054 7996 Dihedral : 4.343 19.150 6278 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.37 % Allowed : 17.80 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5708 helix: 1.26 (0.09), residues: 3156 sheet: -0.69 (0.20), residues: 642 loop : -0.78 (0.15), residues: 1910 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 430 time to evaluate : 5.692 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 outliers start: 13 outliers final: 9 residues processed: 434 average time/residue: 1.1825 time to fit residues: 865.9528 Evaluate side-chains 428 residues out of total 5096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 419 time to evaluate : 5.453 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.8824 time to fit residues: 22.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 373 optimal weight: 6.9990 chunk 500 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 433 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 470 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 483 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 HIS ** B2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.160722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.122063 restraints weight = 544036.947| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 4.16 r_work: 0.4072 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4078 r_free = 0.4078 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 204 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 131 | |-----------------------------------------------------------------------------| r_final: 0.4069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 47018 Z= 0.204 Angle : 0.551 7.884 63872 Z= 0.282 Chirality : 0.037 0.188 7744 Planarity : 0.004 0.092 7996 Dihedral : 4.143 19.594 6278 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.29 % Allowed : 17.98 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 5708 helix: 1.62 (0.09), residues: 3149 sheet: -0.64 (0.20), residues: 640 loop : -0.61 (0.15), residues: 1919 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20720.58 seconds wall clock time: 359 minutes 50.38 seconds (21590.38 seconds total)