Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 10:18:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2d_27832/04_2023/8e2d_27832.pdb" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.093 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 226 5.16 5 C 19790 2.51 5 N 5256 2.21 5 O 5626 1.98 5 H 31562 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1434": "OD1" <-> "OD2" Residue "A TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1460": "OD1" <-> "OD2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "A GLU 1489": "OE1" <-> "OE2" Residue "A GLU 1511": "OE1" <-> "OE2" Residue "A ASP 1811": "OD1" <-> "OD2" Residue "A TYR 1878": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1922": "OE1" <-> "OE2" Residue "A ASP 1943": "OD1" <-> "OD2" Residue "A GLU 1966": "OE1" <-> "OE2" Residue "A PHE 1971": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2060": "OE1" <-> "OE2" Residue "A GLU 2102": "OE1" <-> "OE2" Residue "A GLU 2373": "OE1" <-> "OE2" Residue "A ASP 2391": "OD1" <-> "OD2" Residue "A GLU 2419": "OE1" <-> "OE2" Residue "A ASP 2592": "OD1" <-> "OD2" Residue "A ASP 2875": "OD1" <-> "OD2" Residue "A GLU 3079": "OE1" <-> "OE2" Residue "A ASP 3343": "OD1" <-> "OD2" Residue "A GLU 3345": "OE1" <-> "OE2" Residue "A ASP 3512": "OD1" <-> "OD2" Residue "A GLU 3621": "OE1" <-> "OE2" Residue "A PHE 3642": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3681": "OD1" <-> "OD2" Residue "A PHE 3717": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3965": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3992": "OD1" <-> "OD2" Residue "A TYR 3999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1434": "OD1" <-> "OD2" Residue "B TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1460": "OD1" <-> "OD2" Residue "B GLU 1461": "OE1" <-> "OE2" Residue "B ASP 1811": "OD1" <-> "OD2" Residue "B TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1911": "OD1" <-> "OD2" Residue "B GLU 1922": "OE1" <-> "OE2" Residue "B ASP 1943": "OD1" <-> "OD2" Residue "B ASP 1961": "OD1" <-> "OD2" Residue "B PHE 1971": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2060": "OE1" <-> "OE2" Residue "B GLU 2061": "OE1" <-> "OE2" Residue "B GLU 2102": "OE1" <-> "OE2" Residue "B GLU 2107": "OE1" <-> "OE2" Residue "B ASP 2592": "OD1" <-> "OD2" Residue "B ASP 2875": "OD1" <-> "OD2" Residue "B GLU 2939": "OE1" <-> "OE2" Residue "B TYR 2940": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3034": "OD1" <-> "OD2" Residue "B ASP 3090": "OD1" <-> "OD2" Residue "B ASP 3093": "OD1" <-> "OD2" Residue "B GLU 3345": "OE1" <-> "OE2" Residue "B GLU 3510": "OE1" <-> "OE2" Residue "B ASP 3512": "OD1" <-> "OD2" Residue "B ASP 3518": "OD1" <-> "OD2" Residue "B PHE 3642": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 3717": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 3760": "OE1" <-> "OE2" Residue "B PHE 3789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 3807": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 3818": "OE1" <-> "OE2" Residue "B PHE 3965": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 3980": "OE1" <-> "OE2" Residue "B ASP 3992": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 62460 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 31230 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1968, 31055 Classifications: {'peptide': 1968} Link IDs: {'PTRANS': 88, 'TRANS': 1879} Chain breaks: 31 Conformer: "B" Number of residues, atoms: 1968, 31055 Classifications: {'peptide': 1968} Link IDs: {'PTRANS': 88, 'TRANS': 1879} Chain breaks: 31 bond proxies already assigned to first conformer: 31158 Chain: "B" Number of atoms: 31230 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1968, 31055 Classifications: {'peptide': 1968} Link IDs: {'PTRANS': 88, 'TRANS': 1879} Chain breaks: 31 Conformer: "B" Number of residues, atoms: 1968, 31055 Classifications: {'peptide': 1968} Link IDs: {'PTRANS': 88, 'TRANS': 1879} Chain breaks: 31 bond proxies already assigned to first conformer: 31158 Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N ACYS A2642 " occ=0.81 ... (20 atoms not shown) pdb=" HG BCYS A2642 " occ=0.19 residue: pdb=" N ASER A2703 " occ=0.30 ... (20 atoms not shown) pdb=" HG BSER A2703 " occ=0.70 residue: pdb=" N ASER A2725 " occ=0.09 ... (20 atoms not shown) pdb=" HG BSER A2725 " occ=0.91 residue: pdb=" N ATHR A2748 " occ=0.04 ... (26 atoms not shown) pdb="HG23BTHR A2748 " occ=0.96 residue: pdb=" N AVAL A2753 " occ=0.85 ... (30 atoms not shown) pdb="HG23BVAL A2753 " occ=0.15 residue: pdb=" N ASER A2809 " occ=0.76 ... (20 atoms not shown) pdb=" HG BSER A2809 " occ=0.24 residue: pdb=" N ATHR A3074 " occ=0.30 ... (26 atoms not shown) pdb="HG23BTHR A3074 " occ=0.70 residue: pdb=" N AVAL A3257 " occ=0.48 ... (30 atoms not shown) pdb="HG23BVAL A3257 " occ=0.52 residue: pdb=" N ASER A3368 " occ=0.41 ... (20 atoms not shown) pdb=" HG BSER A3368 " occ=0.59 residue: pdb=" N AILE A3392 " occ=0.65 ... (36 atoms not shown) pdb="HD13BILE A3392 " occ=0.35 residue: pdb=" N ASER B2703 " occ=0.23 ... (20 atoms not shown) pdb=" HG BSER B2703 " occ=0.77 residue: pdb=" N ATHR B2748 " occ=0.18 ... (26 atoms not shown) pdb="HG23BTHR B2748 " occ=0.82 ... (remaining 7 not shown) Time building chain proxies: 39.68, per 1000 atoms: 0.64 Number of scatterers: 62460 At special positions: 0 Unit cell: (139.92, 205.04, 137.28, 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 226 16.00 O 5626 8.00 N 5256 7.00 C 19790 6.00 H 31562 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: 43.26 Conformation dependent library (CDL) restraints added in 8.0 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7560 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 61.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 1018 through 1030 Processing helix chain 'A' and resid 1050 through 1055 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.963A pdb=" N GLN A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 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: 3.685A pdb=" N HIS A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.529A pdb=" N GLN A1343 " --> pdb=" O ASP A1340 " (cutoff:3.500A) 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: 3.683A 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 1437 removed outlier: 4.128A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1442 Processing helix chain 'A' and resid 1444 through 1459 Processing helix chain 'A' and resid 1462 through 1484 removed outlier: 3.677A pdb=" N ARG A1479 " --> pdb=" O THR A1475 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.751A pdb=" N SER A1941 " --> pdb=" O THR A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1960 through 1998 Processing helix chain 'A' and resid 2012 through 2018 Processing helix chain 'A' and resid 2019 through 2040 Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2091 through 2105 Processing helix chain 'A' and resid 2113 through 2128 Processing helix chain 'A' and resid 2132 through 2147 Processing helix chain 'A' and resid 2164 through 2182 Processing helix chain 'A' and resid 2199 through 2204 removed outlier: 4.315A 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: 3.599A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.634A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2400 through 2420 removed outlier: 3.543A pdb=" N ALA A2404 " --> pdb=" O GLY A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2573 Processing helix chain 'A' and resid 2576 through 2599 Processing helix chain 'A' and resid 2635 through 2649 Processing helix chain 'A' and resid 2656 through 2669 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2731 Processing helix chain 'A' and resid 2747 through 2755 Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.028A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2781 through 2802 removed outlier: 4.303A pdb=" N ALA A2785 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 4.020A 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: 3.662A 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: 3.627A 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: 3.651A 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: 3.887A pdb=" N LEU A3183 " --> pdb=" O ALA A3179 " (cutoff:3.500A) removed outlier: 3.672A 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: 3.843A pdb=" N SER A3309 " --> pdb=" O THR A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3321 No H-bonds generated for 'chain 'A' and resid 3321 through 3321' Processing helix chain 'A' and resid 3322 through 3326 Processing helix chain 'A' and resid 3327 through 3340 removed outlier: 3.617A 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: 3.616A pdb=" N ILE A3378 " --> pdb=" O HIS A3374 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3428 through 3441 Processing helix chain 'A' and resid 3445 through 3466 Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3490 through 3506 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.614A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3532 Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3565 removed outlier: 3.973A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A3558 " --> pdb=" O PRO A3554 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3617 Processing helix chain 'A' and resid 3619 through 3630 removed outlier: 3.727A 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: 4.470A 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: 3.865A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A3713 " --> pdb=" O ASN A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 Processing helix chain 'A' and resid 3774 through 3790 Processing helix chain 'A' and resid 3806 through 3816 Processing helix chain 'A' and resid 3846 through 3850 Processing helix chain 'A' and resid 3865 through 3872 Processing helix chain 'A' and resid 3982 through 3993 Processing helix chain 'A' and resid 4069 through 4077 Processing helix chain 'A' and resid 4078 through 4085 removed outlier: 3.550A pdb=" N LEU A4082 " --> pdb=" O GLY A4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1030 Processing helix chain 'B' and resid 1050 through 1055 Processing helix chain 'B' and resid 1060 through 1067 removed outlier: 3.988A 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: 3.681A pdb=" N HIS B1328 " --> pdb=" O PHE B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1343 removed outlier: 3.572A pdb=" N GLN B1343 " --> pdb=" O ASP B1340 " (cutoff:3.500A) 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: 3.683A 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: 4.055A pdb=" N VAL B1427 " --> pdb=" O ALA B1423 " (cutoff:3.500A) removed outlier: 4.369A 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: 3.656A pdb=" N ARG B1479 " --> pdb=" O THR B1475 " (cutoff:3.500A) removed outlier: 3.885A 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: 3.732A 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 2164 through 2182 Processing helix chain 'B' and resid 2199 through 2204 removed outlier: 4.351A 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: 3.598A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.642A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.555A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 3.547A pdb=" N VAL B2573 " --> pdb=" O ARG B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2599 Processing helix chain 'B' and resid 2635 through 2649 Processing helix chain 'B' and resid 2656 through 2669 Processing helix chain 'B' and resid 2697 through 2711 Processing helix chain 'B' and resid 2715 through 2731 Processing helix chain 'B' and resid 2747 through 2755 Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.028A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2781 through 2802 removed outlier: 4.309A pdb=" N ALA B2785 " --> pdb=" O VAL B2781 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2821 removed outlier: 4.023A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2845 removed outlier: 3.656A pdb=" N GLU B2845 " --> pdb=" O GLU B2841 " (cutoff:3.500A) Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2915 through 2931 removed outlier: 3.624A 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: 3.653A 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: 3.887A pdb=" N LEU B3183 " --> pdb=" O ALA B3179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B3184 " --> pdb=" O GLU B3180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3179 through 3184' Processing helix chain 'B' and resid 3231 through 3235 Processing helix chain 'B' and resid 3305 through 3309 removed outlier: 3.845A pdb=" N SER B3309 " --> pdb=" O THR B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3321 No H-bonds generated for 'chain 'B' and resid 3321 through 3321' Processing helix chain 'B' and resid 3322 through 3326 Processing helix chain 'B' and resid 3327 through 3340 removed outlier: 3.650A 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: 3.615A 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: 3.605A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.994A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B3558 " --> pdb=" O PRO B3554 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3617 Processing helix chain 'B' and resid 3619 through 3630 removed outlier: 3.729A 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: 4.496A 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: 3.834A pdb=" N TRP B3712 " --> pdb=" O VAL B3708 " (cutoff:3.500A) removed outlier: 3.731A 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 4085 removed outlier: 3.524A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 6.599A pdb=" N ILE A1120 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A1186 " --> pdb=" O ILE A1120 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A1122 " --> pdb=" O GLY A1184 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY A1184 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A1124 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1564 through 1565 removed outlier: 6.593A pdb=" N HIS A1881 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A1801 " --> pdb=" O HIS A1881 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1569 through 1573 removed outlier: 5.610A pdb=" N CYS A1570 " --> pdb=" O ASP A1794 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP A1794 " --> pdb=" O CYS A1570 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A1572 " --> pdb=" O THR A1792 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A1855 " --> pdb=" O ILE A1819 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A1819 " --> pdb=" O PHE A1855 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS A1857 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A1817 " --> pdb=" O LYS A1857 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A1859 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A1815 " --> pdb=" O THR A1859 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A1861 " --> pdb=" O ALA A1813 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A1815 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1833 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A1817 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1578 through 1580 Processing sheet with id=AA6, first strand: chain 'A' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2879 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 2941 through 2943 removed outlier: 5.167A pdb=" N ALA A2978 " --> pdb=" O LEU A2934 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3855 through 3861 removed outlier: 9.118A pdb=" N ILE A4002 " --> pdb=" O LYS A3821 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A3823 " --> pdb=" O ILE A4002 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A4004 " --> pdb=" O THR A3823 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A3825 " --> pdb=" O LEU A4004 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A4006 " --> pdb=" O PHE A3825 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A3827 " --> pdb=" O VAL A4006 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 6.620A pdb=" N ILE B1120 " --> pdb=" O VAL B1186 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B1186 " --> pdb=" O ILE B1120 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B1122 " --> pdb=" O GLY B1184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B1184 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B1124 " --> pdb=" O LEU B1182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1564 through 1565 removed outlier: 6.612A pdb=" N HIS B1881 " --> pdb=" O LEU B1801 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU B1801 " --> pdb=" O HIS B1881 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1569 through 1573 removed outlier: 5.604A pdb=" N CYS B1570 " --> pdb=" O ASP B1794 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B1794 " --> pdb=" O CYS B1570 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B1572 " --> pdb=" O THR B1792 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE B1855 " --> pdb=" O ILE B1819 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B1819 " --> pdb=" O PHE B1855 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS B1857 " --> pdb=" O ILE B1817 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B1817 " --> pdb=" O LYS B1857 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR B1859 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B1815 " --> pdb=" O THR B1859 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B1861 " --> pdb=" O ALA B1813 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B1815 " --> pdb=" O VAL B1833 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B1833 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B1817 " --> pdb=" O LEU B1831 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1578 through 1580 Processing sheet with id=AB5, 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=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 2941 through 2943 removed outlier: 5.163A pdb=" N ALA B2978 " --> pdb=" O LEU B2934 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3855 through 3861 removed outlier: 9.134A pdb=" N ILE B4002 " --> pdb=" O LYS B3821 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B3823 " --> pdb=" O ILE B4002 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B4004 " --> pdb=" O THR B3823 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B3825 " --> pdb=" O LEU B4004 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B4006 " --> pdb=" O PHE B3825 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B3827 " --> pdb=" O VAL B4006 " (cutoff:3.500A) 1732 hydrogen bonds defined for protein. 5009 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: 24.03 Time building geometry restraints manager: 45.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 31448 1.04 - 1.23: 677 1.23 - 1.43: 12086 1.43 - 1.62: 18515 1.62 - 1.82: 338 Bond restraints: 63064 Sorted by residual: bond pdb=" CA ASP B3209 " pdb=" CB ASP B3209 " ideal model delta sigma weight residual 1.532 1.558 -0.025 1.74e-02 3.30e+03 2.14e+00 bond pdb=" C VAL A2046 " pdb=" N PRO A2047 " ideal model delta sigma weight residual 1.337 1.353 -0.015 1.24e-02 6.50e+03 1.55e+00 bond pdb=" CG ARG A1390 " pdb=" CD ARG A1390 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB PRO A1036 " pdb=" CG PRO A1036 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.18e+00 bond pdb=" C VAL B2046 " pdb=" N PRO B2047 " ideal model delta sigma weight residual 1.337 1.350 -0.013 1.24e-02 6.50e+03 1.16e+00 ... (remaining 63059 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.11: 804 106.11 - 113.13: 76329 113.13 - 120.14: 18543 120.14 - 127.16: 18263 127.16 - 134.18: 427 Bond angle restraints: 114366 Sorted by residual: angle pdb=" C ASP A2164 " pdb=" N ILE A2165 " pdb=" CA ILE A2165 " ideal model delta sigma weight residual 120.24 122.44 -2.20 6.30e-01 2.52e+00 1.22e+01 angle pdb=" C ASP B2164 " pdb=" N ILE B2165 " pdb=" CA ILE B2165 " ideal model delta sigma weight residual 120.24 122.39 -2.15 6.30e-01 2.52e+00 1.17e+01 angle pdb=" C ILE B2165 " pdb=" CA ILE B2165 " pdb=" CB ILE B2165 " ideal model delta sigma weight residual 114.35 110.87 3.48 1.06e+00 8.90e-01 1.08e+01 angle pdb=" C ILE A2165 " pdb=" CA ILE A2165 " pdb=" CB ILE A2165 " ideal model delta sigma weight residual 114.35 110.87 3.48 1.06e+00 8.90e-01 1.08e+01 angle pdb=" CB ARG A1390 " pdb=" CG ARG A1390 " pdb=" CD ARG A1390 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 ... (remaining 114361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 22860 17.89 - 35.78: 1826 35.78 - 53.67: 445 53.67 - 71.56: 122 71.56 - 89.45: 45 Dihedral angle restraints: 25298 sinusoidal: 11966 harmonic: 13332 Sorted by residual: dihedral pdb=" CA PHE B3420 " pdb=" C PHE B3420 " pdb=" N GLY B3421 " pdb=" CA GLY B3421 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PHE A3420 " pdb=" C PHE A3420 " pdb=" N GLY A3421 " pdb=" CA GLY A3421 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLN B1323 " pdb=" C GLN B1323 " pdb=" N PHE B1324 " pdb=" CA PHE B1324 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 25295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3799 0.034 - 0.068: 971 0.068 - 0.102: 268 0.102 - 0.136: 122 0.136 - 0.169: 12 Chirality restraints: 5172 Sorted by residual: chirality pdb=" CB ILE B2807 " pdb=" CA ILE B2807 " pdb=" CG1 ILE B2807 " pdb=" CG2 ILE B2807 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB ILE A2807 " pdb=" CA ILE A2807 " pdb=" CG1 ILE A2807 " pdb=" CG2 ILE A2807 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.96e-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 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 5169 not shown) Planarity restraints: 9090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1390 " 0.252 9.50e-02 1.11e+02 8.44e-02 9.16e+00 pdb=" NE ARG A1390 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A1390 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A1390 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1390 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A1390 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A1390 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A1390 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1390 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B1885 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B1886 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B1886 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B1886 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B3684 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B3685 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B3685 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B3685 " 0.020 5.00e-02 4.00e+02 ... (remaining 9087 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 989 2.05 - 2.69: 100373 2.69 - 3.33: 200041 3.33 - 3.96: 260437 3.96 - 4.60: 403174 Nonbonded interactions: 965014 Sorted by model distance: nonbonded pdb=" O ASN A3535 " pdb=" HZ1 LYS A3540 " model vdw 1.414 1.850 nonbonded pdb=" OE1 GLN A2200 " pdb=" H GLN A2200 " model vdw 1.489 1.850 nonbonded pdb=" O ASN B3535 " pdb=" HZ1 LYS B3540 " model vdw 1.528 1.850 nonbonded pdb=" HZ1 LYS A3624 " pdb=" OD2 ASP A3628 " model vdw 1.529 1.850 nonbonded pdb=" O ARG B1958 " pdb=" HE ARG B1958 " model vdw 1.529 1.850 ... (remaining 965009 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 1010 through 2641 or resid 2644 through 2702 or resid 2705 \ through 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 275 \ 5 through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 30 \ 76 through 3117 or resid 3120 through 3256 or resid 3259 through 3367 or resid 3 \ 369 through 3391 or resid 3394 through 4087)) selection = (chain 'B' and (resid 1010 through 2641 or resid 2644 through 2702 or resid 2705 \ through 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 275 \ 5 through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 30 \ 76 through 3117 or resid 3120 through 3256 or resid 3259 through 3367 or resid 3 \ 369 through 3391 or resid 3394 through 4087)) } 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=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.760 Extract box with map and model: 25.290 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 182.450 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.240 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.003 0.054 31502 Z= 0.174 Angle : 0.562 6.663 42800 Z= 0.303 Chirality : 0.037 0.169 5172 Planarity : 0.004 0.113 5344 Dihedral : 15.751 89.452 11464 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.85 % 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: 1.44 (0.13), residues: 3880 helix: 1.66 (0.11), residues: 2264 sheet: 0.21 (0.27), residues: 348 loop : 0.00 (0.17), residues: 1268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 308 time to evaluate : 3.830 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 outliers start: 28 outliers final: 23 residues processed: 332 average time/residue: 2.1517 time to fit residues: 885.5386 Evaluate side-chains 283 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.5792 time to fit residues: 9.1137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.6980 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1328 HIS ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2687 ASN ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 31502 Z= 0.257 Angle : 0.556 6.432 42800 Z= 0.286 Chirality : 0.038 0.146 5172 Planarity : 0.004 0.069 5344 Dihedral : 4.207 19.059 4160 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.62 % 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: 1.57 (0.13), residues: 3880 helix: 1.78 (0.11), residues: 2278 sheet: 0.27 (0.28), residues: 338 loop : -0.01 (0.18), residues: 1264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 293 average time/residue: 2.1169 time to fit residues: 774.8558 Evaluate side-chains 278 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 8 average time/residue: 0.7883 time to fit residues: 15.2249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 317 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 HIS ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3859 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 31502 Z= 0.258 Angle : 0.551 6.449 42800 Z= 0.282 Chirality : 0.038 0.150 5172 Planarity : 0.004 0.075 5344 Dihedral : 4.216 19.062 4160 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.65 % 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: 1.58 (0.13), residues: 3880 helix: 1.81 (0.11), residues: 2266 sheet: 0.19 (0.28), residues: 348 loop : 0.01 (0.18), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 269 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 37 residues processed: 307 average time/residue: 2.0794 time to fit residues: 803.8929 Evaluate side-chains 290 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 13 average time/residue: 0.8879 time to fit residues: 23.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 357 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2687 ASN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3859 HIS ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1328 HIS ** B1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 31502 Z= 0.327 Angle : 0.585 6.595 42800 Z= 0.302 Chirality : 0.040 0.168 5172 Planarity : 0.005 0.075 5344 Dihedral : 4.348 19.619 4160 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.91 % 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: 1.36 (0.13), residues: 3880 helix: 1.63 (0.11), residues: 2266 sheet: 0.11 (0.28), residues: 344 loop : -0.10 (0.17), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 263 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 35 residues processed: 309 average time/residue: 2.1167 time to fit residues: 820.8722 Evaluate side-chains 285 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 250 time to evaluate : 4.004 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 12 average time/residue: 1.1035 time to fit residues: 24.7332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 ASN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 31502 Z= 0.274 Angle : 0.558 7.158 42800 Z= 0.286 Chirality : 0.039 0.163 5172 Planarity : 0.004 0.081 5344 Dihedral : 4.283 19.200 4160 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.79 % 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: 1.41 (0.13), residues: 3880 helix: 1.71 (0.11), residues: 2268 sheet: -0.07 (0.28), residues: 334 loop : -0.10 (0.17), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 257 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 296 average time/residue: 2.1154 time to fit residues: 781.3749 Evaluate side-chains 289 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 3.772 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 29 residues processed: 11 average time/residue: 0.9431 time to fit residues: 20.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 379 optimal weight: 3.9990 chunk 314 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 31502 Z= 0.194 Angle : 0.518 6.458 42800 Z= 0.263 Chirality : 0.037 0.157 5172 Planarity : 0.004 0.098 5344 Dihedral : 4.100 18.294 4160 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.51 % 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: 1.75 (0.14), residues: 3880 helix: 2.04 (0.11), residues: 2246 sheet: -0.10 (0.28), residues: 348 loop : 0.04 (0.18), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 260 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 299 average time/residue: 2.0761 time to fit residues: 783.8915 Evaluate side-chains 283 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 5 average time/residue: 0.9000 time to fit residues: 11.9090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3322 GLN ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 HIS ** B1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 31502 Z= 0.421 Angle : 0.631 6.719 42800 Z= 0.328 Chirality : 0.044 0.206 5172 Planarity : 0.005 0.087 5344 Dihedral : 4.455 20.212 4160 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.65 % 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: 1.12 (0.13), residues: 3880 helix: 1.48 (0.11), residues: 2258 sheet: 0.11 (0.27), residues: 340 loop : -0.29 (0.17), residues: 1282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 34 residues processed: 297 average time/residue: 2.0704 time to fit residues: 773.5420 Evaluate side-chains 285 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 7 average time/residue: 0.6622 time to fit residues: 13.1151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 240 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 31502 Z= 0.190 Angle : 0.527 6.340 42800 Z= 0.268 Chirality : 0.037 0.146 5172 Planarity : 0.004 0.089 5344 Dihedral : 4.173 18.776 4160 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.39 % 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: 1.60 (0.14), residues: 3880 helix: 1.91 (0.11), residues: 2258 sheet: 0.00 (0.28), residues: 332 loop : -0.10 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 292 average time/residue: 2.0866 time to fit residues: 770.4118 Evaluate side-chains 278 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 4 average time/residue: 0.9716 time to fit residues: 10.8824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 0.8980 chunk 350 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 31502 Z= 0.214 Angle : 0.531 6.479 42800 Z= 0.270 Chirality : 0.037 0.145 5172 Planarity : 0.005 0.102 5344 Dihedral : 4.144 18.359 4160 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.22 % 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: 1.72 (0.14), residues: 3880 helix: 2.05 (0.11), residues: 2240 sheet: -0.03 (0.28), residues: 336 loop : -0.06 (0.17), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 33 residues processed: 283 average time/residue: 2.1104 time to fit residues: 755.4228 Evaluate side-chains 277 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 1.0371 time to fit residues: 9.6299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 390 optimal weight: 0.0470 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 31502 Z= 0.187 Angle : 0.511 6.119 42800 Z= 0.259 Chirality : 0.037 0.145 5172 Planarity : 0.004 0.091 5344 Dihedral : 4.016 17.894 4160 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.14 % 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: 1.86 (0.14), residues: 3880 helix: 2.17 (0.11), residues: 2246 sheet: 0.04 (0.28), residues: 334 loop : -0.04 (0.18), residues: 1300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 282 average time/residue: 2.1286 time to fit residues: 769.1915 Evaluate side-chains 270 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 3.778 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 4.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 8.9990 chunk 331 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 0.0980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125676 restraints weight = 209978.336| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.45 r_work: 0.3442 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 103 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 31502 Z= 0.175 Angle : 0.510 7.194 42800 Z= 0.257 Chirality : 0.036 0.144 5172 Planarity : 0.004 0.114 5344 Dihedral : 3.960 17.373 4160 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3880 helix: 2.25 (0.11), residues: 2246 sheet: -0.03 (0.27), residues: 346 loop : 0.05 (0.18), residues: 1288 =============================================================================== Job complete usr+sys time: 16889.56 seconds wall clock time: 291 minutes 40.63 seconds (17500.63 seconds total)