Starting phenix.real_space_refine on Tue Mar 19 22:24:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2k_27841/03_2024/8e2k_27841.pdb" } resolution = 3.21 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= 0.042 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 309 5.16 5 C 30619 2.51 5 N 8177 2.21 5 O 8798 1.98 5 H 48882 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96785 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 43316 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: 43385 Chain: "B" Number of atoms: 43316 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: 43385 Chain: "X" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4473 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N ACYS A2642 " occ=0.06 ... (20 atoms not shown) pdb=" HG BCYS A2642 " occ=0.06 residue: pdb=" N ASER A2703 " occ=0.18 ... (20 atoms not shown) pdb=" HG BSER A2703 " occ=0.82 residue: pdb=" N ATHR A2748 " occ=0.08 ... (26 atoms not shown) pdb="HG23BTHR A2748 " occ=0.92 residue: pdb=" N AVAL A2753 " occ=0.25 ... (30 atoms not shown) pdb="HG23BVAL A2753 " occ=0.25 residue: pdb=" N ASER A2809 " occ=0.61 ... (20 atoms not shown) pdb=" HG BSER A2809 " occ=0.39 residue: pdb=" N ASER A2820 " occ=0.19 ... (20 atoms not shown) pdb=" HG BSER A2820 " occ=0.81 residue: pdb=" N ATHR A3074 " occ=0.41 ... (26 atoms not shown) pdb="HG23BTHR A3074 " occ=0.59 residue: pdb=" N AILE A3118 " occ=0.00 ... (36 atoms not shown) pdb="HD13BILE A3118 " occ=0.00 residue: pdb=" N ASER A3368 " occ=0.34 ... (20 atoms not shown) pdb=" HG BSER A3368 " occ=0.66 residue: pdb=" N AILE A3392 " occ=0.37 ... (36 atoms not shown) pdb="HD13BILE A3392 " occ=0.37 residue: pdb=" N ACYS B2642 " occ=0.10 ... (20 atoms not shown) pdb=" HG BCYS B2642 " occ=0.10 residue: pdb=" N ASER B2703 " occ=0.28 ... (20 atoms not shown) pdb=" HG BSER B2703 " occ=0.72 ... (remaining 7 not shown) Time building chain proxies: 58.24, per 1000 atoms: 0.60 Number of scatterers: 96785 At special positions: 0 Unit cell: (180, 211.2, 193.2, 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 309 16.00 O 8798 8.00 N 8177 7.00 C 30619 6.00 H 48882 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: 67.86 Conformation dependent library (CDL) restraints added in 14.9 seconds 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11744 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 42 sheets defined 52.3% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.526A pdb=" N PHE A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) 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: 3.681A 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 removed outlier: 3.506A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N THR A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.689A pdb=" N GLN A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.160A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (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: 3.846A pdb=" N GLN A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1073 removed outlier: 3.933A pdb=" N HIS A1073 " --> pdb=" O ASP A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1069 through 1073' 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: 3.878A 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 removed outlier: 3.771A pdb=" N GLU A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1414 Processing helix chain 'A' and resid 1423 through 1436 removed outlier: 3.976A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 Proline residue: A1440 - end of helix No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1444 through 1459 Processing helix chain 'A' and resid 1462 through 1484 removed outlier: 3.655A pdb=" N ARG A1479 " --> pdb=" O THR A1475 " (cutoff:3.500A) removed outlier: 3.957A 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 1823 through 1828 Processing helix chain 'A' and resid 1885 through 1890 Processing helix chain 'A' and resid 1912 through 1941 removed outlier: 3.977A 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 2148 through 2150 No H-bonds generated for 'chain 'A' and resid 2148 through 2150' Processing helix chain 'A' and resid 2164 through 2182 Processing helix chain 'A' and resid 2199 through 2205 removed outlier: 4.362A pdb=" N PHE A2203 " --> pdb=" O GLN A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2342 Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.569A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.694A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2400 through 2420 removed outlier: 3.549A pdb=" N ALA A2404 " --> pdb=" O GLY A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2573 removed outlier: 3.520A pdb=" N GLU A2572 " --> pdb=" O ALA A2569 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 2747 through 2755 Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.080A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A2768 " --> pdb=" O LYS A2764 " (cutoff:3.500A) Processing helix chain 'A' and resid 2781 through 2802 removed outlier: 4.480A pdb=" N ALA A2785 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 4.023A 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 2845 removed outlier: 3.776A pdb=" N GLU A2845 " --> pdb=" O GLU A2841 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2915 through 2931 removed outlier: 3.710A 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: 3.645A 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 3118 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: 3.769A pdb=" N LEU A3183 " --> pdb=" O ALA A3179 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.626A 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: 3.785A pdb=" N LEU A3331 " --> pdb=" O SER A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3341 through 3343 No H-bonds generated for 'chain 'A' and resid 3341 through 3343' Processing helix chain 'A' and resid 3344 through 3353 Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3374 through 3387 removed outlier: 3.842A 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 removed outlier: 3.545A pdb=" N MET A3466 " --> pdb=" O ARG A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3490 through 3508 removed outlier: 3.501A pdb=" N LEU A3508 " --> pdb=" O SER A3504 " (cutoff:3.500A) Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.825A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.797A 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 removed outlier: 3.518A pdb=" N PHE A3522 " --> pdb=" O ASP A3518 " (cutoff:3.500A) Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3565 removed outlier: 3.555A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3617 Processing helix chain 'A' and resid 3619 through 3630 removed outlier: 3.734A pdb=" N GLY A3630 " --> pdb=" O LEU A3626 " (cutoff:3.500A) Processing helix chain 'A' and resid 3630 through 3645 Processing helix chain 'A' and resid 3679 through 3695 removed outlier: 4.315A 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: 3.841A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 3.605A 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 4087 removed outlier: 3.543A 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: 3.629A 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: 3.507A 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 4359 through 4367 Processing helix chain 'A' and resid 4368 through 4378 Processing helix chain 'A' and resid 4381 through 4388 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: 4.102A pdb=" N GLN A4482 " --> pdb=" O VAL A4478 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 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: 3.677A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 285 through 293 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: 3.651A pdb=" N THR B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.828A 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: 3.707A pdb=" N GLN B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 removed outlier: 4.114A pdb=" N GLU B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 728 " --> pdb=" O LYS B 724 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1029 Processing helix chain 'B' and resid 1050 through 1055 Processing helix chain 'B' and resid 1062 through 1067 removed outlier: 3.749A pdb=" N GLN B1065 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1072 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: 3.844A 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 removed outlier: 3.774A pdb=" N GLU B1395 " --> pdb=" O VAL B1391 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1414 Processing helix chain 'B' and resid 1423 through 1437 removed outlier: 4.204A pdb=" N VAL B1427 " --> pdb=" O ALA B1423 " (cutoff:3.500A) removed outlier: 4.368A 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 removed outlier: 3.683A pdb=" N ARG B1479 " --> pdb=" O THR B1475 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B1480 " --> pdb=" O ALA B1476 " (cutoff:3.500A) 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: 3.827A 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 2132 through 2147 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 2199 through 2205 removed outlier: 4.339A pdb=" N PHE B2203 " --> pdb=" O GLN B2200 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2342 Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.568A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) removed outlier: 3.536A 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: 3.672A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.527A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2573 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: 4.098A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2781 through 2802 removed outlier: 4.383A pdb=" N ALA B2785 " --> pdb=" O VAL B2781 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2821 removed outlier: 4.037A 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 2844 Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2915 through 2931 removed outlier: 3.657A 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: 3.595A 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: 3.970A pdb=" N LEU B3183 " --> pdb=" O ALA B3179 " (cutoff:3.500A) removed outlier: 3.695A 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 3229 through 3235 removed outlier: 4.266A pdb=" N LEU B3232 " --> pdb=" O LEU B3229 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B3233 " --> pdb=" O ALA B3230 " (cutoff:3.500A) Processing helix chain 'B' and resid 3305 through 3309 removed outlier: 3.732A 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 3340 removed outlier: 3.557A pdb=" N LEU B3331 " --> pdb=" O SER B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3341 through 3343 No H-bonds generated for 'chain 'B' and resid 3341 through 3343' 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: 3.608A 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 3506 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.719A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.695A 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: 3.641A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3617 Processing helix chain 'B' and resid 3619 through 3630 removed outlier: 3.700A pdb=" N GLY B3630 " --> pdb=" O LEU B3626 " (cutoff:3.500A) Processing helix chain 'B' and resid 3630 through 3645 Processing helix chain 'B' and resid 3679 through 3695 removed outlier: 4.336A 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: 3.871A pdb=" N TRP B3712 " --> pdb=" O VAL B3708 " (cutoff:3.500A) removed outlier: 3.579A 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 Processing helix chain 'B' and resid 3846 through 3850 Processing helix chain 'B' and resid 3865 through 3872 Processing helix chain 'B' and resid 3982 through 3993 Processing helix chain 'B' and resid 4069 through 4077 Processing helix chain 'B' and resid 4078 through 4087 removed outlier: 3.770A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (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 4205 through 4209 removed outlier: 3.651A 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 Processing helix chain 'B' and resid 4242 through 4256 Processing helix chain 'B' and resid 4306 through 4332 Processing helix chain 'B' and resid 4358 through 4367 removed outlier: 4.569A pdb=" N GLU B4362 " --> pdb=" O SER B4358 " (cutoff:3.500A) Processing helix chain 'B' and resid 4368 through 4378 Processing helix chain 'B' and resid 4381 through 4388 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: 4.085A pdb=" N GLN B4482 " --> pdb=" O VAL B4478 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 148 removed outlier: 3.872A pdb=" N ASN X 148 " --> pdb=" O ARG X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 158 Processing helix chain 'X' and resid 335 through 343 Processing helix chain 'X' and resid 370 through 381 removed outlier: 4.051A pdb=" N GLU X 381 " --> pdb=" O LEU X 377 " (cutoff:3.500A) Processing helix chain 'X' and resid 400 through 406 Processing helix chain 'X' and resid 423 through 434 Processing helix chain 'Y' and resid 143 through 148 removed outlier: 3.933A pdb=" N ASN Y 148 " --> pdb=" O ARG Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 158 Processing helix chain 'Y' and resid 196 through 201 removed outlier: 4.014A pdb=" N VAL Y 200 " --> pdb=" O ASN Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 247 through 251 Processing helix chain 'Y' and resid 335 through 343 Processing helix chain 'Z' and resid 143 through 148 Processing helix chain 'Z' and resid 148 through 158 Processing helix chain 'Z' and resid 247 through 251 Processing helix chain 'Z' and resid 335 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.175A pdb=" N ALA A 81 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP A 95 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR A 101 " --> pdb=" O ASP A 95 " (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: 6.543A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 409 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A 423 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 411 " --> pdb=" O HIS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 509 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 504 through 509 current: chain 'A' and resid 566 through 574 removed outlier: 6.534A pdb=" N SER A 634 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.602A 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: 6.810A pdb=" N GLY A 748 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 736 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.830A 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: 6.171A pdb=" N VAL A 912 " --> pdb=" O LYS A 925 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 925 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 6.805A 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 1074 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1074 through 1079 current: chain 'A' and resid 1199 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: 4.868A pdb=" N LEU A1124 " --> pdb=" O GLY A1184 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY A1184 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS A1126 " --> pdb=" O LEU A1182 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU A1182 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1564 through 1565 removed outlier: 6.640A pdb=" N HIS A1881 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 5.151A 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: 5.561A pdb=" N CYS A1570 " --> pdb=" O ASP A1794 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP A1794 " --> pdb=" O CYS A1570 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1572 " --> pdb=" O THR A1792 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A1855 " --> pdb=" O ILE A1819 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A1819 " --> pdb=" O PHE A1855 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A1857 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A1817 " --> pdb=" O LYS A1857 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A1859 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A1815 " --> pdb=" O THR A1859 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A1861 " --> pdb=" O ALA A1813 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A1815 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A1833 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 6.533A 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 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: 5.193A 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 Processing sheet with id=AB9, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.952A pdb=" N ALA B 81 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 91 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA B 104 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 93 " --> pdb=" O LEU B 102 " (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 160 through 166 Processing sheet with id=AC3, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AC4, first strand: chain 'B' and resid 388 through 390 removed outlier: 6.114A pdb=" N ALA B 403 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 409 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS B 423 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 411 " --> pdb=" O HIS B 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 504 through 513 removed outlier: 5.608A pdb=" N LEU B 505 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR B 574 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE B 507 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 572 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 509 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS B 566 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER B 634 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 716 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 731 through 738 removed outlier: 6.711A pdb=" N GLY B 748 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 736 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 746 " --> pdb=" O ILE B 736 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 902 through 903 removed outlier: 5.967A pdb=" N VAL B 912 " --> pdb=" O LYS B 925 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 925 " --> pdb=" O VAL B 912 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 914 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 940 through 945 removed outlier: 6.818A pdb=" N CYS B 955 " --> pdb=" O VAL B 941 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL B 943 " --> pdb=" O CYS B 953 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS B 953 " --> pdb=" O VAL B 943 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR B 945 " --> pdb=" O ARG B 951 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG B 951 " --> pdb=" O TYR B 945 " (cutoff:3.500A) Processing sheet with id=AC9, 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=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 6.737A pdb=" N ILE B1120 " --> pdb=" O VAL B1186 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B1186 " --> pdb=" O ILE B1120 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B1122 " --> pdb=" O GLY B1184 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY B1184 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B1124 " --> pdb=" O LEU B1182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1564 through 1565 removed outlier: 6.608A pdb=" N HIS B1881 " --> pdb=" O LEU B1801 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU B1801 " --> pdb=" O HIS B1881 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1569 through 1573 removed outlier: 6.657A pdb=" N THR B1792 " --> pdb=" O VAL B1571 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B1573 " --> pdb=" O PHE B1790 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE B1790 " --> pdb=" O THR B1573 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE B1855 " --> pdb=" O ILE B1819 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B1819 " --> pdb=" O PHE B1855 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS B1857 " --> pdb=" O ILE B1817 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B1817 " --> pdb=" O LYS B1857 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR B1859 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B1815 " --> pdb=" O THR B1859 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B1861 " --> pdb=" O ALA B1813 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B1815 " --> pdb=" O VAL B1833 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B1833 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B1817 " --> pdb=" O LEU B1831 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1578 through 1580 Processing sheet with id=AD5, 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=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 2941 through 2943 removed outlier: 5.300A pdb=" N ALA B2978 " --> pdb=" O LEU B2934 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 3855 through 3861 removed outlier: 9.273A pdb=" N ILE B4002 " --> pdb=" O LYS B3821 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B3823 " --> pdb=" O ILE B4002 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B4004 " --> pdb=" O THR B3823 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B3825 " --> pdb=" O LEU B4004 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B4006 " --> pdb=" O PHE B3825 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN B3827 " --> pdb=" O VAL B4006 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 161 through 169 removed outlier: 7.045A pdb=" N ASP X 168 " --> pdb=" O PRO X 178 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N SER X 183 " --> pdb=" O ASN X 196 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN X 196 " --> pdb=" O SER X 183 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU X 192 " --> pdb=" O VAL X 187 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG X 233 " --> pdb=" O VAL X 220 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL X 220 " --> pdb=" O ARG X 233 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N ARG X 205 " --> pdb=" O LEU X 167 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU X 167 " --> pdb=" O ARG X 205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 271 through 274 removed outlier: 3.750A pdb=" N THR X 271 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN X 312 " --> pdb=" O VAL X 317 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL X 317 " --> pdb=" O ASN X 312 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR X 322 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE X 333 " --> pdb=" O THR X 322 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS X 324 " --> pdb=" O PHE X 331 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE X 331 " --> pdb=" O LYS X 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 359 through 361 Processing sheet with id=AE2, first strand: chain 'X' and resid 364 through 368 removed outlier: 6.619A pdb=" N MET X 365 " --> pdb=" O HIS X 394 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 419 through 420 current: chain 'X' and resid 446 through 452 Processing sheet with id=AE3, first strand: chain 'Y' and resid 161 through 170 removed outlier: 6.885A pdb=" N ASP Y 168 " --> pdb=" O PRO Y 178 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N HIS Y 170 " --> pdb=" O GLU Y 176 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU Y 176 " --> pdb=" O HIS Y 170 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU Y 192 " --> pdb=" O VAL Y 187 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG Y 233 " --> pdb=" O VAL Y 220 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL Y 220 " --> pdb=" O ARG Y 233 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N ARG Y 205 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU Y 167 " --> pdb=" O ARG Y 205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 271 through 274 removed outlier: 3.882A pdb=" N THR Y 271 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN Y 312 " --> pdb=" O VAL Y 317 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL Y 317 " --> pdb=" O ASN Y 312 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR Y 322 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE Y 333 " --> pdb=" O THR Y 322 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS Y 324 " --> pdb=" O PHE Y 331 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE Y 331 " --> pdb=" O LYS Y 324 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 161 through 169 removed outlier: 6.354A pdb=" N ASP Z 168 " --> pdb=" O PRO Z 178 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU Z 192 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG Z 233 " --> pdb=" O VAL Z 220 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL Z 220 " --> pdb=" O ARG Z 233 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N ARG Z 205 " --> pdb=" O LEU Z 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU Z 167 " --> pdb=" O ARG Z 205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 271 through 274 removed outlier: 3.664A pdb=" N THR Z 271 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN Z 312 " --> pdb=" O VAL Z 317 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL Z 317 " --> pdb=" O ASN Z 312 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR Z 322 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE Z 333 " --> pdb=" O THR Z 322 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS Z 324 " --> pdb=" O PHE Z 331 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE Z 331 " --> pdb=" O LYS Z 324 " (cutoff:3.500A) 2513 hydrogen bonds defined for protein. 7214 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: 47.49 Time building geometry restraints manager: 71.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 48716 1.03 - 1.23: 190 1.23 - 1.42: 19478 1.42 - 1.62: 28849 1.62 - 1.82: 452 Bond restraints: 97685 Sorted by residual: bond pdb=" CG GLU X 381 " pdb=" CD GLU X 381 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.52e+00 bond pdb=" CB GLU X 381 " pdb=" CG GLU X 381 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.23e+00 bond pdb=" CG ASN B2670 " pdb=" ND2 ASN B2670 " ideal model delta sigma weight residual 1.328 1.293 0.035 2.10e-02 2.27e+03 2.77e+00 bond pdb=" CA ARG X 380 " pdb=" C ARG X 380 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.35e-02 5.49e+03 2.60e+00 bond pdb=" C ASP A1896 " pdb=" O ASP A1896 " ideal model delta sigma weight residual 1.235 1.242 -0.007 4.70e-03 4.53e+04 2.47e+00 ... (remaining 97680 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.21: 1505 106.21 - 113.18: 118653 113.18 - 120.15: 28645 120.15 - 127.12: 27767 127.12 - 134.08: 649 Bond angle restraints: 177219 Sorted by residual: angle pdb=" CB ARG B1958 " pdb=" CG ARG B1958 " pdb=" CD ARG B1958 " ideal model delta sigma weight residual 111.30 118.43 -7.13 2.30e+00 1.89e-01 9.61e+00 angle pdb=" CA VAL X 325 " pdb=" C VAL X 325 " pdb=" N THR X 326 " ideal model delta sigma weight residual 116.60 120.20 -3.60 1.45e+00 4.76e-01 6.15e+00 angle pdb=" N PRO B 397 " pdb=" CA PRO B 397 " pdb=" C PRO B 397 " ideal model delta sigma weight residual 114.92 112.00 2.92 1.19e+00 7.06e-01 6.01e+00 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 119.80 -7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" C ALA A2709 " pdb=" N TRP A2710 " pdb=" CA TRP A2710 " ideal model delta sigma weight residual 122.26 118.29 3.97 1.73e+00 3.34e-01 5.25e+00 ... (remaining 177214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 41402 17.76 - 35.53: 3037 35.53 - 53.29: 1053 53.29 - 71.05: 287 71.05 - 88.82: 62 Dihedral angle restraints: 45841 sinusoidal: 25262 harmonic: 20579 Sorted by residual: dihedral pdb=" CA ASN X 268 " pdb=" C ASN X 268 " pdb=" N THR X 269 " pdb=" CA THR X 269 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN Z 268 " pdb=" C ASN Z 268 " pdb=" N THR Z 269 " pdb=" CA THR Z 269 " ideal model delta harmonic sigma weight residual 180.00 151.76 28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA MET X 323 " pdb=" C MET X 323 " pdb=" N LYS X 324 " pdb=" CA LYS X 324 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 45838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 6334 0.046 - 0.092: 1306 0.092 - 0.138: 375 0.138 - 0.184: 16 0.184 - 0.230: 1 Chirality restraints: 8032 Sorted by residual: chirality pdb=" CA ASN B2670 " pdb=" N ASN B2670 " pdb=" C ASN B2670 " pdb=" CB ASN B2670 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU B4307 " pdb=" N GLU B4307 " pdb=" C GLU B4307 " pdb=" CB GLU B4307 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE B1780 " pdb=" N ILE B1780 " pdb=" C ILE B1780 " pdb=" CB ILE B1780 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 8029 not shown) Planarity restraints: 14121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1554 " 0.012 2.00e-02 2.50e+03 4.74e-02 6.75e+01 pdb=" CG PHE A1554 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A1554 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE A1554 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A1554 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 PHE A1554 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A1554 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A1554 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A1554 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A1554 " 0.101 2.00e-02 2.50e+03 pdb=" HE2 PHE A1554 " -0.010 2.00e-02 2.50e+03 pdb=" HZ PHE A1554 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1554 " -0.001 2.00e-02 2.50e+03 3.80e-02 4.34e+01 pdb=" CG PHE B1554 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B1554 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE B1554 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE B1554 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B1554 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B1554 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE B1554 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE B1554 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE B1554 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 PHE B1554 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B1554 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 303 " 0.003 2.00e-02 2.50e+03 2.51e-02 1.89e+01 pdb=" CG PHE X 303 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE X 303 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE X 303 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE X 303 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 PHE X 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE X 303 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 PHE X 303 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 PHE X 303 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 PHE X 303 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE X 303 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE X 303 " -0.021 2.00e-02 2.50e+03 ... (remaining 14118 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 1673 2.07 - 2.70: 160461 2.70 - 3.33: 298205 3.33 - 3.97: 377699 3.97 - 4.60: 594637 Nonbonded interactions: 1432675 Sorted by model distance: nonbonded pdb=" H HIS A3374 " pdb=" OE2 GLU X 381 " model vdw 1.432 1.850 nonbonded pdb=" OE1 GLN B2200 " pdb=" H GLN B2200 " model vdw 1.506 1.850 nonbonded pdb=" O ALA A2688 " pdb="HD21 ASN A2731 " model vdw 1.507 1.850 nonbonded pdb=" OE1 GLU B4063 " pdb=" H GLU B4063 " model vdw 1.510 1.850 nonbonded pdb="HH21 ARG A1406 " pdb=" OE1 GLU A2580 " model vdw 1.511 1.850 ... (remaining 1432670 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 1405 or (resid 1406 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) \ or resid 1407 through 1865 or (resid 1866 and (name N or name CA or name C or na \ me O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or r \ esid 1867 through 2641 or resid 2644 through 2702 or resid 2705 through 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 o \ r resid 3120 through 3367 or resid 3369 through 3391 or resid 3394 through 4499) \ ) selection = (chain 'B' and (resid 68 through 2569 or (resid 2570 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) \ or resid 2571 through 2586 or (resid 2587 and (name N or name CA or name C or na \ me O or name CB or name OG or name H or name HA or name HB2 or name HB3)) or res \ id 2588 through 2641 or resid 2644 through 2702 or resid 2705 through 2724 or re \ sid 2727 through 2747 or resid 2750 through 2752 or resid 2755 through 2808 or r \ esid 2811 through 2819 or resid 2822 through 3073 or resid 3076 through 3117 or \ resid 3120 through 3367 or resid 3369 through 3391 or resid 3394 through 4499)) } ncs_group { reference = chain 'Y' selection = chain 'Z' } 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: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 1.200 Extract box with map and model: 13.050 Check model and map are aligned: 1.090 Set scattering table: 0.700 Process input model: 302.550 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 328.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 0.059 48803 Z= 0.259 Angle : 0.614 7.130 66318 Z= 0.326 Chirality : 0.041 0.230 8032 Planarity : 0.006 0.109 8322 Dihedral : 15.389 88.817 17779 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 0.83 % Allowed : 15.19 % Favored : 83.98 % 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: 1.10 (0.11), residues: 6016 helix: 1.93 (0.10), residues: 2935 sheet: -0.57 (0.18), residues: 841 loop : -0.30 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A2710 HIS 0.009 0.001 HIS X 198 PHE 0.040 0.002 PHE X 303 TYR 0.022 0.002 TYR X 216 ARG 0.022 0.001 ARG B3281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 590 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 549 time to evaluate : 5.674 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: A 636 LYS cc_start: 0.1426 (tptm) cc_final: 0.0653 (tmmt) REVERT: A 1783 MET cc_start: 0.5030 (tpt) cc_final: 0.4436 (tmm) REVERT: A 2576 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6301 (pm20) REVERT: A 3711 LEU cc_start: 0.9284 (tm) cc_final: 0.9074 (tm) REVERT: A 3824 MET cc_start: 0.8164 (tpp) cc_final: 0.7728 (tpp) REVERT: A 3864 THR cc_start: 0.8156 (m) cc_final: 0.7747 (m) REVERT: A 3871 ASP cc_start: 0.7724 (m-30) cc_final: 0.7517 (t70) REVERT: B 1212 MET cc_start: 0.3445 (ttm) cc_final: 0.3243 (ttm) REVERT: B 1321 MET cc_start: 0.4266 (mtm) cc_final: 0.3983 (mtp) REVERT: B 1324 PHE cc_start: 0.6960 (m-10) cc_final: 0.6758 (m-80) REVERT: B 1358 TRP cc_start: 0.6450 (t60) cc_final: 0.6237 (t60) REVERT: B 1512 MET cc_start: 0.8775 (tpp) cc_final: 0.8275 (tpt) REVERT: B 1781 GLU cc_start: 0.5671 (mt-10) cc_final: 0.4914 (pm20) REVERT: B 1856 MET cc_start: 0.8693 (mtp) cc_final: 0.8120 (tpp) REVERT: B 3193 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7039 (ttm170) REVERT: B 3543 ASP cc_start: 0.8472 (m-30) cc_final: 0.8133 (m-30) REVERT: B 3981 MET cc_start: 0.8331 (ttp) cc_final: 0.7849 (tpp) REVERT: B 4314 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7182 (mmt180) REVERT: B 4413 LEU cc_start: 0.5173 (pp) cc_final: 0.4754 (mp) REVERT: B 4452 ARG cc_start: 0.5419 (mtt180) cc_final: 0.4510 (tpp-160) REVERT: Y 177 VAL cc_start: 0.3754 (t) cc_final: 0.3478 (t) outliers start: 41 outliers final: 8 residues processed: 587 average time/residue: 1.2598 time to fit residues: 1191.2222 Evaluate side-chains 314 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 306 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 1399 SER Chi-restraints excluded: chain X residue 232 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 387 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 517 optimal weight: 10.0000 chunk 464 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 480 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 556 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2670 ASN A3283 HIS A3975 GLN B 222 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3055 GLN B3790 GLN Y 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 48803 Z= 0.295 Angle : 0.594 6.376 66318 Z= 0.311 Chirality : 0.040 0.208 8032 Planarity : 0.004 0.061 8322 Dihedral : 4.581 58.380 6521 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.45 % Rotamer: Outliers : 1.24 % Allowed : 16.00 % Favored : 82.76 % 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: 6016 helix: 1.93 (0.09), residues: 2951 sheet: -0.55 (0.18), residues: 810 loop : -0.25 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2710 HIS 0.012 0.001 HIS A 348 PHE 0.020 0.002 PHE A3807 TYR 0.015 0.001 TYR B2870 ARG 0.008 0.001 ARG B1390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 317 time to evaluate : 6.600 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: A 1436 MET cc_start: 0.8972 (ttt) cc_final: 0.8596 (ttp) REVERT: A 2592 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 3871 ASP cc_start: 0.7563 (m-30) cc_final: 0.7227 (t70) REVERT: B 1324 PHE cc_start: 0.7220 (m-10) cc_final: 0.7013 (m-80) REVERT: B 1512 MET cc_start: 0.8636 (tpp) cc_final: 0.8295 (tpt) REVERT: B 1781 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5047 (pm20) REVERT: B 1817 ILE cc_start: 0.8824 (mt) cc_final: 0.8551 (mt) REVERT: B 2326 GLU cc_start: 0.8742 (mp0) cc_final: 0.8159 (tm-30) REVERT: B 3543 ASP cc_start: 0.8454 (m-30) cc_final: 0.8131 (m-30) REVERT: B 4413 LEU cc_start: 0.5192 (pp) cc_final: 0.4710 (mp) REVERT: B 4452 ARG cc_start: 0.5460 (mtt180) cc_final: 0.4524 (tpp-160) outliers start: 63 outliers final: 30 residues processed: 373 average time/residue: 1.3268 time to fit residues: 823.2471 Evaluate side-chains 322 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3343 ASP Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 4245 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1345 THR Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 4217 LEU Chi-restraints excluded: chain X residue 232 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain X residue 387 VAL Chi-restraints excluded: chain Y residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 309 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 463 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 557 optimal weight: 0.0370 chunk 602 optimal weight: 20.0000 chunk 496 optimal weight: 5.9990 chunk 553 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1435 ASN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 146 GLN Z 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48803 Z= 0.239 Angle : 0.549 8.324 66318 Z= 0.283 Chirality : 0.039 0.162 8032 Planarity : 0.004 0.055 8322 Dihedral : 4.355 58.349 6517 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 1.09 % Allowed : 15.80 % Favored : 83.11 % 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: 1.19 (0.11), residues: 6016 helix: 1.99 (0.09), residues: 2953 sheet: -0.50 (0.18), residues: 814 loop : -0.27 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2710 HIS 0.013 0.001 HIS A3099 PHE 0.016 0.001 PHE B1407 TYR 0.016 0.001 TYR A1457 ARG 0.007 0.000 ARG B1390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 361 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 306 time to evaluate : 5.770 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: A 1783 MET cc_start: 0.5019 (tpt) cc_final: 0.4412 (tmm) REVERT: A 2592 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 3871 ASP cc_start: 0.7438 (m-30) cc_final: 0.7075 (t70) REVERT: B 1012 LEU cc_start: 0.3774 (mt) cc_final: 0.3442 (mt) REVERT: B 1512 MET cc_start: 0.8691 (tpp) cc_final: 0.8315 (tpt) REVERT: B 1781 GLU cc_start: 0.6045 (mt-10) cc_final: 0.5082 (pm20) REVERT: B 3030 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.7725 (mm) REVERT: B 3543 ASP cc_start: 0.8458 (m-30) cc_final: 0.8132 (m-30) REVERT: B 3848 MET cc_start: 0.8644 (ppp) cc_final: 0.8413 (ppp) REVERT: B 4413 LEU cc_start: 0.5302 (pp) cc_final: 0.4763 (mp) REVERT: B 4452 ARG cc_start: 0.5617 (mtt180) cc_final: 0.4632 (tpp-160) outliers start: 55 outliers final: 33 residues processed: 349 average time/residue: 1.1957 time to fit residues: 696.4063 Evaluate side-chains 324 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1916 MET Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1345 THR Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 4217 LEU Chi-restraints excluded: chain X residue 232 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain X residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 550 optimal weight: 10.0000 chunk 419 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 559 optimal weight: 10.0000 chunk 592 optimal weight: 20.0000 chunk 292 optimal weight: 10.0000 chunk 530 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN ** A1435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3161 HIS A3527 ASN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 GLN ** B1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1328 HIS B1845 HIS ** B2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 ASN B2733 GLN B4379 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 48803 Z= 0.565 Angle : 0.783 9.572 66318 Z= 0.418 Chirality : 0.047 0.368 8032 Planarity : 0.006 0.060 8322 Dihedral : 5.155 54.380 6517 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 1.90 % Allowed : 15.41 % Favored : 82.68 % 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: -0.56 (0.10), residues: 6016 helix: 0.36 (0.09), residues: 2967 sheet: -0.86 (0.18), residues: 834 loop : -1.04 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A2710 HIS 0.016 0.003 HIS A3099 PHE 0.033 0.003 PHE B2704 TYR 0.031 0.003 TYR B3060 ARG 0.013 0.001 ARG A2075 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 281 time to evaluate : 5.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.1634 (mmm) cc_final: 0.1357 (mtp) REVERT: A 1436 MET cc_start: 0.8965 (ttt) cc_final: 0.8590 (ttp) REVERT: A 2893 PHE cc_start: 0.4469 (OUTLIER) cc_final: 0.4263 (m-80) REVERT: A 3507 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8666 (tt) REVERT: A 3871 ASP cc_start: 0.7925 (m-30) cc_final: 0.7236 (t70) REVERT: B 1321 MET cc_start: 0.3765 (mtp) cc_final: 0.3318 (mtp) REVERT: B 1512 MET cc_start: 0.8875 (tpp) cc_final: 0.8464 (tpt) REVERT: B 2326 GLU cc_start: 0.8742 (mp0) cc_final: 0.8174 (tm-30) REVERT: B 3543 ASP cc_start: 0.8666 (m-30) cc_final: 0.8369 (m-30) REVERT: B 4452 ARG cc_start: 0.5680 (mtt180) cc_final: 0.4641 (tpp-160) REVERT: X 260 MET cc_start: 0.4652 (tpp) cc_final: 0.4433 (tpp) outliers start: 97 outliers final: 57 residues processed: 362 average time/residue: 1.2318 time to fit residues: 749.3473 Evaluate side-chains 320 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 1916 MET Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2577 GLN Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3093 ASP Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3676 MET Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4245 HIS Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1345 THR Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2084 GLN Chi-restraints excluded: chain B residue 2381 GLU Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 2928 ILE Chi-restraints excluded: chain B residue 3093 ASP Chi-restraints excluded: chain B residue 3101 MET Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 3753 THR Chi-restraints excluded: chain B residue 4217 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 316 GLU Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain X residue 387 VAL Chi-restraints excluded: chain Y residue 181 ASN Chi-restraints excluded: chain Z residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 493 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 441 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 505 optimal weight: 5.9990 chunk 409 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 302 optimal weight: 20.0000 chunk 531 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1771 GLN A2077 HIS ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48803 Z= 0.225 Angle : 0.564 6.100 66318 Z= 0.292 Chirality : 0.039 0.161 8032 Planarity : 0.004 0.055 8322 Dihedral : 4.609 53.916 6515 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 1.15 % Allowed : 16.17 % Favored : 82.68 % 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: 0.34 (0.11), residues: 6016 helix: 1.25 (0.09), residues: 2966 sheet: -0.66 (0.18), residues: 831 loop : -0.73 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2710 HIS 0.008 0.001 HIS A4215 PHE 0.020 0.001 PHE B1407 TYR 0.015 0.001 TYR A1457 ARG 0.007 0.000 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 271 time to evaluate : 5.741 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: A 309 MET cc_start: 0.1572 (mmm) cc_final: 0.1296 (mtp) REVERT: A 1212 MET cc_start: 0.5597 (ttm) cc_final: 0.4955 (ttm) REVERT: A 1436 MET cc_start: 0.8854 (ttt) cc_final: 0.8651 (ttp) REVERT: A 1512 MET cc_start: 0.8460 (tpt) cc_final: 0.7907 (mmm) REVERT: A 1783 MET cc_start: 0.5043 (tpt) cc_final: 0.4611 (tmm) REVERT: A 2592 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7712 (t0) REVERT: A 2893 PHE cc_start: 0.4432 (OUTLIER) cc_final: 0.4206 (m-80) REVERT: A 3871 ASP cc_start: 0.7622 (m-30) cc_final: 0.6982 (t70) REVERT: B 2326 GLU cc_start: 0.8720 (mp0) cc_final: 0.8154 (tm-30) REVERT: B 3543 ASP cc_start: 0.8526 (m-30) cc_final: 0.8213 (m-30) REVERT: B 3848 MET cc_start: 0.8660 (ppp) cc_final: 0.8439 (ppp) REVERT: B 4452 ARG cc_start: 0.5770 (mtt180) cc_final: 0.4708 (tpp-160) outliers start: 56 outliers final: 43 residues processed: 316 average time/residue: 1.2263 time to fit residues: 648.3176 Evaluate side-chains 303 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 258 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1916 MET Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2577 GLN Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2581 LEU Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3052 MET Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain X residue 387 VAL Chi-restraints excluded: chain Y residue 337 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 199 optimal weight: 6.9990 chunk 533 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 593 optimal weight: 20.0000 chunk 492 optimal weight: 0.9980 chunk 274 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 311 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1771 GLN A2577 GLN ** A3618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1771 GLN ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 48803 Z= 0.320 Angle : 0.600 7.051 66318 Z= 0.311 Chirality : 0.040 0.156 8032 Planarity : 0.004 0.054 8322 Dihedral : 4.574 52.670 6515 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.81 % Favored : 95.18 % Rotamer: Outliers : 1.63 % Allowed : 15.86 % Favored : 82.52 % 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: 0.34 (0.11), residues: 6016 helix: 1.25 (0.09), residues: 2967 sheet: -0.56 (0.18), residues: 797 loop : -0.79 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2710 HIS 0.014 0.001 HIS B4319 PHE 0.018 0.002 PHE B1407 TYR 0.017 0.002 TYR B1457 ARG 0.007 0.001 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 260 time to evaluate : 5.732 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: A 309 MET cc_start: 0.1585 (mmm) cc_final: 0.1310 (mtp) REVERT: A 1512 MET cc_start: 0.8423 (tpt) cc_final: 0.7973 (mmm) REVERT: A 1783 MET cc_start: 0.5079 (tpt) cc_final: 0.4580 (tmm) REVERT: A 2893 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.4411 (m-80) REVERT: A 3507 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 3564 MET cc_start: 0.8561 (mtm) cc_final: 0.8149 (mtp) REVERT: A 3824 MET cc_start: 0.8163 (tpp) cc_final: 0.7509 (tpp) REVERT: A 3871 ASP cc_start: 0.7653 (m-30) cc_final: 0.6973 (t70) REVERT: B 2326 GLU cc_start: 0.8777 (mp0) cc_final: 0.8166 (tm-30) REVERT: B 3030 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 3543 ASP cc_start: 0.8532 (m-30) cc_final: 0.8211 (m-30) outliers start: 82 outliers final: 59 residues processed: 331 average time/residue: 1.1952 time to fit residues: 663.2993 Evaluate side-chains 320 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 258 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 2172 VAL Chi-restraints excluded: chain A residue 2577 GLN Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4193 ASP Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain A residue 4448 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1345 THR Chi-restraints excluded: chain B residue 1771 GLN Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3170 THR Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 3691 THR Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain X residue 387 VAL Chi-restraints excluded: chain Y residue 181 ASN Chi-restraints excluded: chain Y residue 231 THR Chi-restraints excluded: chain Y residue 337 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 571 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 433 optimal weight: 0.7980 chunk 335 optimal weight: 5.9990 chunk 499 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 590 optimal weight: 9.9990 chunk 369 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 272 optimal weight: 0.0770 overall best weight: 2.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1771 GLN A3695 ASN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1567 HIS B1771 GLN ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 48803 Z= 0.243 Angle : 0.553 8.534 66318 Z= 0.285 Chirality : 0.039 0.159 8032 Planarity : 0.004 0.053 8322 Dihedral : 4.453 51.893 6515 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 1.44 % Allowed : 16.12 % Favored : 82.44 % 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: 0.59 (0.11), residues: 6016 helix: 1.50 (0.09), residues: 2961 sheet: -0.50 (0.19), residues: 791 loop : -0.71 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2710 HIS 0.008 0.001 HIS B2653 PHE 0.025 0.001 PHE B4164 TYR 0.013 0.001 TYR B1457 ARG 0.005 0.000 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 260 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1512 MET cc_start: 0.8440 (tpt) cc_final: 0.8014 (mmm) REVERT: A 1783 MET cc_start: 0.5107 (tpt) cc_final: 0.4578 (tmm) REVERT: A 2592 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7706 (t0) REVERT: A 3507 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8629 (tt) REVERT: A 3871 ASP cc_start: 0.7569 (m-30) cc_final: 0.6816 (t70) REVERT: B 1934 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7796 (tpp80) REVERT: B 2326 GLU cc_start: 0.8794 (mp0) cc_final: 0.8251 (tm-30) REVERT: B 3543 ASP cc_start: 0.8495 (m-30) cc_final: 0.8168 (m-30) outliers start: 72 outliers final: 55 residues processed: 322 average time/residue: 1.2003 time to fit residues: 648.8802 Evaluate side-chains 316 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 258 time to evaluate : 5.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 2577 GLN Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 3002 ASN Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain A residue 4448 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1934 ARG Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3160 ILE Chi-restraints excluded: chain B residue 3170 THR Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 3691 THR Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 387 VAL Chi-restraints excluded: chain Y residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 365 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 375 optimal weight: 0.9990 chunk 402 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1771 GLN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1567 HIS ** B1771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 48803 Z= 0.238 Angle : 0.544 8.419 66318 Z= 0.279 Chirality : 0.039 0.175 8032 Planarity : 0.004 0.052 8322 Dihedral : 4.342 50.599 6515 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.65 % Rotamer: Outliers : 1.20 % Allowed : 16.24 % Favored : 82.55 % 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: 0.73 (0.11), residues: 6016 helix: 1.64 (0.09), residues: 2965 sheet: -0.50 (0.19), residues: 791 loop : -0.64 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2710 HIS 0.010 0.001 HIS B4319 PHE 0.018 0.001 PHE B1407 TYR 0.016 0.001 TYR B1457 ARG 0.004 0.000 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 263 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1512 MET cc_start: 0.8424 (tpt) cc_final: 0.8033 (mmm) REVERT: A 2592 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7689 (t0) REVERT: A 3507 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 3871 ASP cc_start: 0.7498 (m-30) cc_final: 0.6756 (t70) REVERT: A 4440 MET cc_start: 0.5581 (tpp) cc_final: 0.5321 (tpp) REVERT: B 2326 GLU cc_start: 0.8779 (mp0) cc_final: 0.8244 (tm-30) REVERT: B 3030 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 3543 ASP cc_start: 0.8489 (m-30) cc_final: 0.8176 (m-30) REVERT: B 3623 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8783 (tt) outliers start: 58 outliers final: 48 residues processed: 315 average time/residue: 1.2122 time to fit residues: 640.4179 Evaluate side-chains 308 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3002 ASN Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 3864 THR Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain A residue 4448 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3160 ILE Chi-restraints excluded: chain B residue 3170 THR Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3643 CYS Chi-restraints excluded: chain B residue 3691 THR Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain Y residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 537 optimal weight: 9.9990 chunk 566 optimal weight: 8.9990 chunk 516 optimal weight: 8.9990 chunk 550 optimal weight: 10.0000 chunk 565 optimal weight: 0.8980 chunk 331 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 432 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 497 optimal weight: 2.9990 chunk 520 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1771 GLN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48803 Z= 0.205 Angle : 0.528 9.472 66318 Z= 0.270 Chirality : 0.039 0.155 8032 Planarity : 0.004 0.052 8322 Dihedral : 4.236 49.734 6514 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.44 % Rotamer: Outliers : 1.29 % Allowed : 16.17 % Favored : 82.54 % 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: 0.90 (0.11), residues: 6016 helix: 1.81 (0.09), residues: 2960 sheet: -0.49 (0.19), residues: 804 loop : -0.57 (0.14), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2710 HIS 0.019 0.001 HIS B4319 PHE 0.019 0.001 PHE B1407 TYR 0.013 0.001 TYR B1457 ARG 0.005 0.000 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 265 time to evaluate : 5.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1512 MET cc_start: 0.8414 (tpt) cc_final: 0.8098 (mmm) REVERT: A 2592 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7775 (t0) REVERT: A 3507 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 3871 ASP cc_start: 0.7574 (m-30) cc_final: 0.6815 (t70) REVERT: B 2326 GLU cc_start: 0.8760 (mp0) cc_final: 0.8240 (tm-30) REVERT: B 3030 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8183 (mm) REVERT: B 3543 ASP cc_start: 0.8491 (m-30) cc_final: 0.8180 (m-30) REVERT: B 3623 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8794 (tt) outliers start: 63 outliers final: 53 residues processed: 321 average time/residue: 1.1835 time to fit residues: 640.2935 Evaluate side-chains 316 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 259 time to evaluate : 6.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3002 ASN Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 4167 LEU Chi-restraints excluded: chain A residue 4193 ASP Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain A residue 4448 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3160 ILE Chi-restraints excluded: chain B residue 3168 THR Chi-restraints excluded: chain B residue 3170 THR Chi-restraints excluded: chain B residue 3251 LEU Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3691 THR Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 316 GLU Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain Y residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 548 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 582 optimal weight: 20.0000 chunk 355 optimal weight: 3.9990 chunk 276 optimal weight: 20.0000 chunk 404 optimal weight: 1.9990 chunk 610 optimal weight: 30.0000 chunk 562 optimal weight: 2.9990 chunk 486 optimal weight: 1.9990 chunk 50 optimal weight: 40.0000 chunk 375 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1771 GLN A1951 ASN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3838 ASN ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48803 Z= 0.261 Angle : 0.548 9.274 66318 Z= 0.283 Chirality : 0.039 0.153 8032 Planarity : 0.004 0.053 8322 Dihedral : 4.278 48.852 6514 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 1.24 % Allowed : 16.26 % Favored : 82.50 % 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: 0.77 (0.11), residues: 6016 helix: 1.68 (0.09), residues: 2965 sheet: -0.49 (0.19), residues: 780 loop : -0.64 (0.14), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2710 HIS 0.020 0.001 HIS B4319 PHE 0.017 0.001 PHE B1407 TYR 0.022 0.001 TYR A1457 ARG 0.004 0.000 ARG A2075 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12032 Ramachandran restraints generated. 6016 Oldfield, 0 Emsley, 6016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2587 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 5.883 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: A 1512 MET cc_start: 0.8411 (tpt) cc_final: 0.8087 (mmm) REVERT: A 3507 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8590 (tt) REVERT: B 2326 GLU cc_start: 0.8744 (mp0) cc_final: 0.8130 (tm-30) REVERT: B 3030 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8248 (mm) REVERT: B 3543 ASP cc_start: 0.8497 (m-30) cc_final: 0.8181 (m-30) outliers start: 60 outliers final: 55 residues processed: 323 average time/residue: 1.2600 time to fit residues: 688.7017 Evaluate side-chains 318 residues out of total 5355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 7.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1784 HIS Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 2172 VAL Chi-restraints excluded: chain A residue 2592 ASP Chi-restraints excluded: chain A residue 2850 VAL Chi-restraints excluded: chain A residue 2893 PHE Chi-restraints excluded: chain A residue 3002 ASN Chi-restraints excluded: chain A residue 3124 SER Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3160 ILE Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3251 LEU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3507 LEU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3780 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3858 LEU Chi-restraints excluded: chain A residue 4193 ASP Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4369 LEU Chi-restraints excluded: chain A residue 4448 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1968 SER Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2124 ILE Chi-restraints excluded: chain B residue 2381 GLU Chi-restraints excluded: chain B residue 2833 LEU Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3124 SER Chi-restraints excluded: chain B residue 3160 ILE Chi-restraints excluded: chain B residue 3168 THR Chi-restraints excluded: chain B residue 3170 THR Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3623 ILE Chi-restraints excluded: chain B residue 3691 THR Chi-restraints excluded: chain X residue 247 ARG Chi-restraints excluded: chain X residue 316 GLU Chi-restraints excluded: chain X residue 386 ASP Chi-restraints excluded: chain Y residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 298 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 518 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 448 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 135 optimal weight: 0.4980 chunk 487 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 500 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1771 GLN ** A4215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1895 HIS ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.135292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.096095 restraints weight = 725394.205| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 4.63 r_work: 0.3695 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 205 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 148 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48803 Z= 0.208 Angle : 0.525 9.522 66318 Z= 0.268 Chirality : 0.039 0.155 8032 Planarity : 0.004 0.051 8322 Dihedral : 4.193 48.468 6514 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.34 % Rotamer: Outliers : 1.20 % Allowed : 16.39 % Favored : 82.41 % 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: 0.97 (0.11), residues: 6016 helix: 1.86 (0.09), residues: 2966 sheet: -0.44 (0.19), residues: 760 loop : -0.55 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2710 HIS 0.019 0.001 HIS B4319 PHE 0.019 0.001 PHE B1407 TYR 0.013 0.001 TYR B1457 ARG 0.003 0.000 ARG A2075 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18565.52 seconds wall clock time: 324 minutes 11.09 seconds (19451.09 seconds total)