Starting phenix.real_space_refine on Wed Oct 28 13:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.map" model { file = "/net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ec_75645/10_2026/11ec_75645.cif" } resolution = 3.22 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 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= 0.008 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 17604 2.51 5 N 4728 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27804 Number of models: 1 Model: "" Number of chains: 1 Chain: "AG" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2317 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 276} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR Time building chain proxies: 3.41, per 1000 atoms: 0.12 Number of scatterers: 27804 At special positions: 0 Unit cell: (141.4, 144.2, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5340 8.00 N 4728 7.00 C 17604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 48 sheets defined 30.1% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'AG' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAG 15 " --> pdb=" O GLYAG 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAG 17 " --> pdb=" O GLYAG 14 " (cutoff:3.500A) Processing helix chain 'AG' and resid 35 through 39 removed outlier: 3.747A pdb=" N THRAG 38 " --> pdb=" O ASNAG 35 " (cutoff:3.500A) Processing helix chain 'AG' and resid 58 through 63 Processing helix chain 'AG' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAG 81 " --> pdb=" O LEUAG 77 " (cutoff:3.500A) Processing helix chain 'AG' and resid 128 through 130 No H-bonds generated for 'chain 'AG' and resid 128 through 130' Processing helix chain 'AG' and resid 131 through 145 Processing helix chain 'AG' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAG 158 " --> pdb=" O LEUAG 155 " (cutoff:3.500A) Processing helix chain 'AG' and resid 168 through 173 removed outlier: 4.227A pdb=" N SERAG 173 " --> pdb=" O ASPAG 170 " (cutoff:3.500A) Processing helix chain 'AG' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAG 240 " --> pdb=" O ALAAG 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAG 241 " --> pdb=" O PHEAG 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAG 244 " --> pdb=" O ARGAG 240 " (cutoff:3.500A) Processing helix chain 'AG' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAG 255 " --> pdb=" O PROAG 252 " (cutoff:3.500A) Processing helix chain 'AG' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAG 269 " --> pdb=" O ALAAG 265 " (cutoff:3.500A) Processing helix chain 'AH' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAH 15 " --> pdb=" O GLYAH 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAH 17 " --> pdb=" O GLYAH 14 " (cutoff:3.500A) Processing helix chain 'AH' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAH 38 " --> pdb=" O ASNAH 35 " (cutoff:3.500A) Processing helix chain 'AH' and resid 58 through 63 Processing helix chain 'AH' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAH 81 " --> pdb=" O LEUAH 77 " (cutoff:3.500A) Processing helix chain 'AH' and resid 128 through 130 No H-bonds generated for 'chain 'AH' and resid 128 through 130' Processing helix chain 'AH' and resid 131 through 145 Processing helix chain 'AH' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAH 158 " --> pdb=" O LEUAH 155 " (cutoff:3.500A) Processing helix chain 'AH' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAH 173 " --> pdb=" O ASPAH 170 " (cutoff:3.500A) Processing helix chain 'AH' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAH 240 " --> pdb=" O ALAAH 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUAH 241 " --> pdb=" O PHEAH 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAH 244 " --> pdb=" O ARGAH 240 " (cutoff:3.500A) Processing helix chain 'AH' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAH 255 " --> pdb=" O PROAH 252 " (cutoff:3.500A) Processing helix chain 'AH' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAH 269 " --> pdb=" O ALAAH 265 " (cutoff:3.500A) Processing helix chain 'AI' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAI 15 " --> pdb=" O GLYAI 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAI 17 " --> pdb=" O GLYAI 14 " (cutoff:3.500A) Processing helix chain 'AI' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAI 38 " --> pdb=" O ASNAI 35 " (cutoff:3.500A) Processing helix chain 'AI' and resid 58 through 63 Processing helix chain 'AI' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAI 81 " --> pdb=" O LEUAI 77 " (cutoff:3.500A) Processing helix chain 'AI' and resid 128 through 130 No H-bonds generated for 'chain 'AI' and resid 128 through 130' Processing helix chain 'AI' and resid 131 through 145 Processing helix chain 'AI' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAI 158 " --> pdb=" O LEUAI 155 " (cutoff:3.500A) Processing helix chain 'AI' and resid 168 through 173 removed outlier: 4.225A pdb=" N SERAI 173 " --> pdb=" O ASPAI 170 " (cutoff:3.500A) Processing helix chain 'AI' and resid 231 through 244 removed outlier: 3.622A pdb=" N ARGAI 240 " --> pdb=" O ALAAI 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAI 241 " --> pdb=" O PHEAI 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAI 244 " --> pdb=" O ARGAI 240 " (cutoff:3.500A) Processing helix chain 'AI' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAI 255 " --> pdb=" O PROAI 252 " (cutoff:3.500A) Processing helix chain 'AI' and resid 263 through 269 removed outlier: 4.050A pdb=" N GLNAI 269 " --> pdb=" O ALAAI 265 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAJ 15 " --> pdb=" O GLYAJ 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAJ 17 " --> pdb=" O GLYAJ 14 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 35 through 39 removed outlier: 3.747A pdb=" N THRAJ 38 " --> pdb=" O ASNAJ 35 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 58 through 63 Processing helix chain 'AJ' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAJ 81 " --> pdb=" O LEUAJ 77 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 128 through 130 No H-bonds generated for 'chain 'AJ' and resid 128 through 130' Processing helix chain 'AJ' and resid 131 through 145 Processing helix chain 'AJ' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAJ 158 " --> pdb=" O LEUAJ 155 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAJ 173 " --> pdb=" O ASPAJ 170 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 231 through 244 removed outlier: 3.620A pdb=" N ARGAJ 240 " --> pdb=" O ALAAJ 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAJ 241 " --> pdb=" O PHEAJ 237 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYSAJ 244 " --> pdb=" O ARGAJ 240 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 251 through 255 removed outlier: 3.619A pdb=" N ARGAJ 255 " --> pdb=" O PROAJ 252 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAJ 269 " --> pdb=" O ALAAJ 265 " (cutoff:3.500A) Processing helix chain 'AK' and resid 11 through 17 removed outlier: 3.649A pdb=" N ALAAK 15 " --> pdb=" O GLYAK 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAK 17 " --> pdb=" O GLYAK 14 " (cutoff:3.500A) Processing helix chain 'AK' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAK 38 " --> pdb=" O ASNAK 35 " (cutoff:3.500A) Processing helix chain 'AK' and resid 58 through 63 Processing helix chain 'AK' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAK 81 " --> pdb=" O LEUAK 77 " (cutoff:3.500A) Processing helix chain 'AK' and resid 128 through 130 No H-bonds generated for 'chain 'AK' and resid 128 through 130' Processing helix chain 'AK' and resid 131 through 145 Processing helix chain 'AK' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAK 158 " --> pdb=" O LEUAK 155 " (cutoff:3.500A) Processing helix chain 'AK' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAK 173 " --> pdb=" O ASPAK 170 " (cutoff:3.500A) Processing helix chain 'AK' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAK 240 " --> pdb=" O ALAAK 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUAK 241 " --> pdb=" O PHEAK 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAK 244 " --> pdb=" O ARGAK 240 " (cutoff:3.500A) Processing helix chain 'AK' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAK 255 " --> pdb=" O PROAK 252 " (cutoff:3.500A) Processing helix chain 'AK' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAK 269 " --> pdb=" O ALAAK 265 " (cutoff:3.500A) Processing helix chain 'AL' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAL 15 " --> pdb=" O GLYAL 12 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SERAL 17 " --> pdb=" O GLYAL 14 " (cutoff:3.500A) Processing helix chain 'AL' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAL 38 " --> pdb=" O ASNAL 35 " (cutoff:3.500A) Processing helix chain 'AL' and resid 58 through 63 Processing helix chain 'AL' and resid 66 through 81 removed outlier: 3.656A pdb=" N VALAL 81 " --> pdb=" O LEUAL 77 " (cutoff:3.500A) Processing helix chain 'AL' and resid 128 through 130 No H-bonds generated for 'chain 'AL' and resid 128 through 130' Processing helix chain 'AL' and resid 131 through 145 Processing helix chain 'AL' and resid 154 through 158 removed outlier: 3.557A pdb=" N ILEAL 158 " --> pdb=" O LEUAL 155 " (cutoff:3.500A) Processing helix chain 'AL' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAL 173 " --> pdb=" O ASPAL 170 " (cutoff:3.500A) Processing helix chain 'AL' and resid 231 through 244 removed outlier: 3.620A pdb=" N ARGAL 240 " --> pdb=" O ALAAL 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAL 241 " --> pdb=" O PHEAL 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAL 244 " --> pdb=" O ARGAL 240 " (cutoff:3.500A) Processing helix chain 'AL' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAL 255 " --> pdb=" O PROAL 252 " (cutoff:3.500A) Processing helix chain 'AL' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAL 269 " --> pdb=" O ALAAL 265 " (cutoff:3.500A) Processing helix chain 'AM' and resid 11 through 17 removed outlier: 3.651A pdb=" N ALAAM 15 " --> pdb=" O GLYAM 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAM 17 " --> pdb=" O GLYAM 14 " (cutoff:3.500A) Processing helix chain 'AM' and resid 35 through 39 removed outlier: 3.747A pdb=" N THRAM 38 " --> pdb=" O ASNAM 35 " (cutoff:3.500A) Processing helix chain 'AM' and resid 58 through 63 Processing helix chain 'AM' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAM 81 " --> pdb=" O LEUAM 77 " (cutoff:3.500A) Processing helix chain 'AM' and resid 128 through 130 No H-bonds generated for 'chain 'AM' and resid 128 through 130' Processing helix chain 'AM' and resid 131 through 145 Processing helix chain 'AM' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAM 158 " --> pdb=" O LEUAM 155 " (cutoff:3.500A) Processing helix chain 'AM' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAM 173 " --> pdb=" O ASPAM 170 " (cutoff:3.500A) Processing helix chain 'AM' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAM 240 " --> pdb=" O ALAAM 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAM 241 " --> pdb=" O PHEAM 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAM 244 " --> pdb=" O ARGAM 240 " (cutoff:3.500A) Processing helix chain 'AM' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAM 255 " --> pdb=" O PROAM 252 " (cutoff:3.500A) Processing helix chain 'AM' and resid 263 through 269 removed outlier: 4.050A pdb=" N GLNAM 269 " --> pdb=" O ALAAM 265 " (cutoff:3.500A) Processing helix chain 'AN' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAN 15 " --> pdb=" O GLYAN 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAN 17 " --> pdb=" O GLYAN 14 " (cutoff:3.500A) Processing helix chain 'AN' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAN 38 " --> pdb=" O ASNAN 35 " (cutoff:3.500A) Processing helix chain 'AN' and resid 58 through 63 Processing helix chain 'AN' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAN 81 " --> pdb=" O LEUAN 77 " (cutoff:3.500A) Processing helix chain 'AN' and resid 128 through 130 No H-bonds generated for 'chain 'AN' and resid 128 through 130' Processing helix chain 'AN' and resid 131 through 145 Processing helix chain 'AN' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAN 158 " --> pdb=" O LEUAN 155 " (cutoff:3.500A) Processing helix chain 'AN' and resid 168 through 173 removed outlier: 4.227A pdb=" N SERAN 173 " --> pdb=" O ASPAN 170 " (cutoff:3.500A) Processing helix chain 'AN' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAN 240 " --> pdb=" O ALAAN 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAN 241 " --> pdb=" O PHEAN 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAN 244 " --> pdb=" O ARGAN 240 " (cutoff:3.500A) Processing helix chain 'AN' and resid 251 through 255 removed outlier: 3.619A pdb=" N ARGAN 255 " --> pdb=" O PROAN 252 " (cutoff:3.500A) Processing helix chain 'AN' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAN 269 " --> pdb=" O ALAAN 265 " (cutoff:3.500A) Processing helix chain 'AO' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAO 15 " --> pdb=" O GLYAO 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAO 17 " --> pdb=" O GLYAO 14 " (cutoff:3.500A) Processing helix chain 'AO' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAO 38 " --> pdb=" O ASNAO 35 " (cutoff:3.500A) Processing helix chain 'AO' and resid 58 through 63 Processing helix chain 'AO' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAO 81 " --> pdb=" O LEUAO 77 " (cutoff:3.500A) Processing helix chain 'AO' and resid 128 through 130 No H-bonds generated for 'chain 'AO' and resid 128 through 130' Processing helix chain 'AO' and resid 131 through 145 Processing helix chain 'AO' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAO 158 " --> pdb=" O LEUAO 155 " (cutoff:3.500A) Processing helix chain 'AO' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAO 173 " --> pdb=" O ASPAO 170 " (cutoff:3.500A) Processing helix chain 'AO' and resid 231 through 244 removed outlier: 3.622A pdb=" N ARGAO 240 " --> pdb=" O ALAAO 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAO 241 " --> pdb=" O PHEAO 237 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYSAO 244 " --> pdb=" O ARGAO 240 " (cutoff:3.500A) Processing helix chain 'AO' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAO 255 " --> pdb=" O PROAO 252 " (cutoff:3.500A) Processing helix chain 'AO' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAO 269 " --> pdb=" O ALAAO 265 " (cutoff:3.500A) Processing helix chain 'AP' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAP 15 " --> pdb=" O GLYAP 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAP 17 " --> pdb=" O GLYAP 14 " (cutoff:3.500A) Processing helix chain 'AP' and resid 35 through 39 removed outlier: 3.747A pdb=" N THRAP 38 " --> pdb=" O ASNAP 35 " (cutoff:3.500A) Processing helix chain 'AP' and resid 58 through 63 Processing helix chain 'AP' and resid 66 through 81 removed outlier: 3.654A pdb=" N VALAP 81 " --> pdb=" O LEUAP 77 " (cutoff:3.500A) Processing helix chain 'AP' and resid 128 through 130 No H-bonds generated for 'chain 'AP' and resid 128 through 130' Processing helix chain 'AP' and resid 131 through 145 Processing helix chain 'AP' and resid 154 through 158 removed outlier: 3.557A pdb=" N ILEAP 158 " --> pdb=" O LEUAP 155 " (cutoff:3.500A) Processing helix chain 'AP' and resid 168 through 173 removed outlier: 4.227A pdb=" N SERAP 173 " --> pdb=" O ASPAP 170 " (cutoff:3.500A) Processing helix chain 'AP' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAP 240 " --> pdb=" O ALAAP 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUAP 241 " --> pdb=" O PHEAP 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAP 244 " --> pdb=" O ARGAP 240 " (cutoff:3.500A) Processing helix chain 'AP' and resid 251 through 255 removed outlier: 3.620A pdb=" N ARGAP 255 " --> pdb=" O PROAP 252 " (cutoff:3.500A) Processing helix chain 'AP' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAP 269 " --> pdb=" O ALAAP 265 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAQ 15 " --> pdb=" O GLYAQ 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAQ 17 " --> pdb=" O GLYAQ 14 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAQ 38 " --> pdb=" O ASNAQ 35 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 58 through 63 Processing helix chain 'AQ' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAQ 81 " --> pdb=" O LEUAQ 77 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 128 through 130 No H-bonds generated for 'chain 'AQ' and resid 128 through 130' Processing helix chain 'AQ' and resid 131 through 145 Processing helix chain 'AQ' and resid 154 through 158 removed outlier: 3.557A pdb=" N ILEAQ 158 " --> pdb=" O LEUAQ 155 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAQ 173 " --> pdb=" O ASPAQ 170 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 231 through 244 removed outlier: 3.621A pdb=" N ARGAQ 240 " --> pdb=" O ALAAQ 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUAQ 241 " --> pdb=" O PHEAQ 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAQ 244 " --> pdb=" O ARGAQ 240 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 251 through 255 removed outlier: 3.619A pdb=" N ARGAQ 255 " --> pdb=" O PROAQ 252 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAQ 269 " --> pdb=" O ALAAQ 265 " (cutoff:3.500A) Processing helix chain 'AR' and resid 11 through 17 removed outlier: 3.650A pdb=" N ALAAR 15 " --> pdb=" O GLYAR 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERAR 17 " --> pdb=" O GLYAR 14 " (cutoff:3.500A) Processing helix chain 'AR' and resid 35 through 39 removed outlier: 3.746A pdb=" N THRAR 38 " --> pdb=" O ASNAR 35 " (cutoff:3.500A) Processing helix chain 'AR' and resid 58 through 63 Processing helix chain 'AR' and resid 66 through 81 removed outlier: 3.655A pdb=" N VALAR 81 " --> pdb=" O LEUAR 77 " (cutoff:3.500A) Processing helix chain 'AR' and resid 128 through 130 No H-bonds generated for 'chain 'AR' and resid 128 through 130' Processing helix chain 'AR' and resid 131 through 145 Processing helix chain 'AR' and resid 154 through 158 removed outlier: 3.556A pdb=" N ILEAR 158 " --> pdb=" O LEUAR 155 " (cutoff:3.500A) Processing helix chain 'AR' and resid 168 through 173 removed outlier: 4.226A pdb=" N SERAR 173 " --> pdb=" O ASPAR 170 " (cutoff:3.500A) Processing helix chain 'AR' and resid 231 through 244 removed outlier: 3.620A pdb=" N ARGAR 240 " --> pdb=" O ALAAR 236 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAR 241 " --> pdb=" O PHEAR 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSAR 244 " --> pdb=" O ARGAR 240 " (cutoff:3.500A) Processing helix chain 'AR' and resid 251 through 255 removed outlier: 3.619A pdb=" N ARGAR 255 " --> pdb=" O PROAR 252 " (cutoff:3.500A) Processing helix chain 'AR' and resid 263 through 269 removed outlier: 4.049A pdb=" N GLNAR 269 " --> pdb=" O ALAAR 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AG' and resid 7 through 8 removed outlier: 4.901A pdb=" N METAG 21 " --> pdb=" O LEUAG 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AG' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAG 175 " --> pdb=" O LEUAG 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAG 190 " --> pdb=" O GLUAG 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAG 195 " --> pdb=" O LEUAG 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AG' and resid 219 through 223 removed outlier: 4.642A pdb=" N GLYAG 87 " --> pdb=" O SERAL 207 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SERAL 207 " --> pdb=" O GLYAG 87 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLNAG 89 " --> pdb=" O TRPAL 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TRPAL 205 " --> pdb=" O GLNAG 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AG' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAG 93 " --> pdb=" O VALAG 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAG 114 " --> pdb=" O GLUAG 93 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLUAG 95 " --> pdb=" O SERAG 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AG' and resid 205 through 209 removed outlier: 6.993A pdb=" N TRPAG 205 " --> pdb=" O GLNAH 89 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLNAH 89 " --> pdb=" O TRPAG 205 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SERAG 207 " --> pdb=" O GLYAH 87 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLYAH 87 " --> pdb=" O SERAG 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AH' and resid 7 through 8 removed outlier: 4.902A pdb=" N METAH 21 " --> pdb=" O LEUAH 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AH' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAH 175 " --> pdb=" O LEUAH 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASNAH 190 " --> pdb=" O GLUAH 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAH 195 " --> pdb=" O LEUAH 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AH' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAH 93 " --> pdb=" O VALAH 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAH 114 " --> pdb=" O GLUAH 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAH 95 " --> pdb=" O SERAH 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AH' and resid 205 through 209 removed outlier: 6.902A pdb=" N TRPAH 205 " --> pdb=" O GLNAI 89 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLNAI 89 " --> pdb=" O TRPAH 205 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SERAH 207 " --> pdb=" O GLYAI 87 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLYAI 87 " --> pdb=" O SERAH 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AI' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAI 21 " --> pdb=" O LEUAI 8 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AI' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAI 175 " --> pdb=" O LEUAI 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASNAI 190 " --> pdb=" O GLUAI 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAI 195 " --> pdb=" O LEUAI 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'AI' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAI 93 " --> pdb=" O VALAI 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAI 114 " --> pdb=" O GLUAI 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAI 95 " --> pdb=" O SERAI 112 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'AI' and resid 205 through 209 removed outlier: 6.879A pdb=" N TRPAI 205 " --> pdb=" O GLNAJ 89 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLNAJ 89 " --> pdb=" O TRPAI 205 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SERAI 207 " --> pdb=" O GLYAJ 87 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLYAJ 87 " --> pdb=" O SERAI 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'AJ' and resid 7 through 8 removed outlier: 4.902A pdb=" N METAJ 21 " --> pdb=" O LEUAJ 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AJ' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAJ 175 " --> pdb=" O LEUAJ 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAJ 190 " --> pdb=" O GLUAJ 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAJ 195 " --> pdb=" O LEUAJ 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'AJ' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAJ 93 " --> pdb=" O VALAJ 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAJ 114 " --> pdb=" O GLUAJ 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAJ 95 " --> pdb=" O SERAJ 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'AJ' and resid 205 through 209 removed outlier: 7.002A pdb=" N TRPAJ 205 " --> pdb=" O GLNAK 89 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLNAK 89 " --> pdb=" O TRPAJ 205 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SERAJ 207 " --> pdb=" O GLYAK 87 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLYAK 87 " --> pdb=" O SERAJ 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'AK' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAK 21 " --> pdb=" O LEUAK 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'AK' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAK 175 " --> pdb=" O LEUAK 55 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASNAK 190 " --> pdb=" O GLUAK 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAK 195 " --> pdb=" O LEUAK 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'AK' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAK 93 " --> pdb=" O VALAK 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAK 114 " --> pdb=" O GLUAK 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAK 95 " --> pdb=" O SERAK 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'AK' and resid 205 through 209 removed outlier: 6.928A pdb=" N TRPAK 205 " --> pdb=" O GLNAL 89 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLNAL 89 " --> pdb=" O TRPAK 205 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SERAK 207 " --> pdb=" O GLYAL 87 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLYAL 87 " --> pdb=" O SERAK 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AL' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAL 21 " --> pdb=" O LEUAL 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AL' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAL 175 " --> pdb=" O LEUAL 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAL 190 " --> pdb=" O GLUAL 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAL 195 " --> pdb=" O LEUAL 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'AL' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAL 93 " --> pdb=" O VALAL 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAL 114 " --> pdb=" O GLUAL 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAL 95 " --> pdb=" O SERAL 112 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'AM' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAM 21 " --> pdb=" O LEUAM 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'AM' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAM 175 " --> pdb=" O LEUAM 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAM 190 " --> pdb=" O GLUAM 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THRAM 195 " --> pdb=" O LEUAM 227 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AM' and resid 219 through 223 removed outlier: 3.560A pdb=" N ILEAM 85 " --> pdb=" O ARGAR 209 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLYAM 87 " --> pdb=" O SERAR 207 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SERAR 207 " --> pdb=" O GLYAM 87 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLNAM 89 " --> pdb=" O TRPAR 205 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TRPAR 205 " --> pdb=" O GLNAM 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'AM' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAM 93 " --> pdb=" O VALAM 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAM 114 " --> pdb=" O GLUAM 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAM 95 " --> pdb=" O SERAM 112 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'AM' and resid 205 through 209 removed outlier: 6.964A pdb=" N TRPAM 205 " --> pdb=" O GLNAN 89 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLNAN 89 " --> pdb=" O TRPAM 205 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SERAM 207 " --> pdb=" O GLYAN 87 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLYAN 87 " --> pdb=" O SERAM 207 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'AN' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAN 21 " --> pdb=" O LEUAN 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'AN' and resid 51 through 56 removed outlier: 6.664A pdb=" N THRAN 175 " --> pdb=" O LEUAN 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASNAN 190 " --> pdb=" O GLUAN 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THRAN 195 " --> pdb=" O LEUAN 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'AN' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAN 93 " --> pdb=" O VALAN 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAN 114 " --> pdb=" O GLUAN 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAN 95 " --> pdb=" O SERAN 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'AN' and resid 205 through 209 removed outlier: 7.003A pdb=" N TRPAN 205 " --> pdb=" O GLNAO 89 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLNAO 89 " --> pdb=" O TRPAN 205 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SERAN 207 " --> pdb=" O GLYAO 87 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLYAO 87 " --> pdb=" O SERAN 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'AO' and resid 7 through 8 removed outlier: 4.902A pdb=" N METAO 21 " --> pdb=" O LEUAO 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AO' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAO 175 " --> pdb=" O LEUAO 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASNAO 190 " --> pdb=" O GLUAO 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THRAO 195 " --> pdb=" O LEUAO 227 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'AO' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAO 93 " --> pdb=" O VALAO 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAO 114 " --> pdb=" O GLUAO 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAO 95 " --> pdb=" O SERAO 112 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'AO' and resid 205 through 209 removed outlier: 7.061A pdb=" N TRPAO 205 " --> pdb=" O GLNAP 89 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLNAP 89 " --> pdb=" O TRPAO 205 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SERAO 207 " --> pdb=" O GLYAP 87 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLYAP 87 " --> pdb=" O SERAO 207 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AP' and resid 7 through 8 removed outlier: 4.902A pdb=" N METAP 21 " --> pdb=" O LEUAP 8 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'AP' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAP 175 " --> pdb=" O LEUAP 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAP 190 " --> pdb=" O GLUAP 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAP 195 " --> pdb=" O LEUAP 227 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'AP' and resid 93 through 100 removed outlier: 6.753A pdb=" N GLUAP 93 " --> pdb=" O VALAP 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAP 114 " --> pdb=" O GLUAP 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAP 95 " --> pdb=" O SERAP 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'AP' and resid 205 through 209 removed outlier: 6.954A pdb=" N TRPAP 205 " --> pdb=" O GLNAQ 89 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLNAQ 89 " --> pdb=" O TRPAP 205 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N SERAP 207 " --> pdb=" O GLYAQ 87 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLYAQ 87 " --> pdb=" O SERAP 207 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'AQ' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAQ 21 " --> pdb=" O LEUAQ 8 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'AQ' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAQ 175 " --> pdb=" O LEUAQ 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASNAQ 190 " --> pdb=" O GLUAQ 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAQ 195 " --> pdb=" O LEUAQ 227 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'AQ' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAQ 93 " --> pdb=" O VALAQ 114 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALAQ 114 " --> pdb=" O GLUAQ 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAQ 95 " --> pdb=" O SERAQ 112 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AQ' and resid 205 through 209 removed outlier: 7.012A pdb=" N TRPAQ 205 " --> pdb=" O GLNAR 89 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLNAR 89 " --> pdb=" O TRPAQ 205 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N SERAQ 207 " --> pdb=" O GLYAR 87 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLYAR 87 " --> pdb=" O SERAQ 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'AR' and resid 7 through 8 removed outlier: 4.903A pdb=" N METAR 21 " --> pdb=" O LEUAR 8 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AR' and resid 51 through 56 removed outlier: 6.665A pdb=" N THRAR 175 " --> pdb=" O LEUAR 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNAR 190 " --> pdb=" O GLUAR 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRAR 195 " --> pdb=" O LEUAR 227 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'AR' and resid 93 through 100 removed outlier: 6.754A pdb=" N GLUAR 93 " --> pdb=" O VALAR 114 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VALAR 114 " --> pdb=" O GLUAR 93 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLUAR 95 " --> pdb=" O SERAR 112 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 1944 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: 4.42 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9312 1.34 - 1.46: 5336 1.46 - 1.57: 13552 1.57 - 1.69: 0 1.69 - 1.80: 240 Bond restraints: 28440 Sorted by residual: bond pdb=" CA VALAI 81 " pdb=" CB VALAI 81 " ideal model delta sigma weight residual 1.544 1.539 0.005 1.17e-02 7.31e+03 1.94e-01 bond pdb=" CA VALAO 81 " pdb=" CB VALAO 81 " ideal model delta sigma weight residual 1.544 1.539 0.005 1.17e-02 7.31e+03 1.93e-01 bond pdb=" CA VALAQ 81 " pdb=" CB VALAQ 81 " ideal model delta sigma weight residual 1.544 1.539 0.005 1.17e-02 7.31e+03 1.88e-01 bond pdb=" CA VALAJ 81 " pdb=" CB VALAJ 81 " ideal model delta sigma weight residual 1.544 1.539 0.005 1.17e-02 7.31e+03 1.81e-01 bond pdb=" CA VALAN 81 " pdb=" CB VALAN 81 " ideal model delta sigma weight residual 1.544 1.539 0.005 1.17e-02 7.31e+03 1.76e-01 ... (remaining 28435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 36742 0.79 - 1.58: 1547 1.58 - 2.37: 231 2.37 - 3.16: 192 3.16 - 3.95: 36 Bond angle restraints: 38748 Sorted by residual: angle pdb=" C GLUAM 80 " pdb=" N VALAM 81 " pdb=" CA VALAM 81 " ideal model delta sigma weight residual 122.35 120.50 1.85 1.18e+00 7.18e-01 2.47e+00 angle pdb=" C GLUAN 80 " pdb=" N VALAN 81 " pdb=" CA VALAN 81 " ideal model delta sigma weight residual 122.35 120.51 1.84 1.18e+00 7.18e-01 2.43e+00 angle pdb=" C GLUAK 80 " pdb=" N VALAK 81 " pdb=" CA VALAK 81 " ideal model delta sigma weight residual 122.35 120.52 1.83 1.18e+00 7.18e-01 2.40e+00 angle pdb=" C GLUAJ 80 " pdb=" N VALAJ 81 " pdb=" CA VALAJ 81 " ideal model delta sigma weight residual 122.35 120.52 1.83 1.18e+00 7.18e-01 2.39e+00 angle pdb=" C GLUAG 80 " pdb=" N VALAG 81 " pdb=" CA VALAG 81 " ideal model delta sigma weight residual 122.35 120.53 1.82 1.18e+00 7.18e-01 2.39e+00 ... (remaining 38743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.14: 16135 11.14 - 22.28: 713 22.28 - 33.41: 168 33.41 - 44.55: 48 44.55 - 55.69: 36 Dihedral angle restraints: 17100 sinusoidal: 6768 harmonic: 10332 Sorted by residual: dihedral pdb=" N LEUAP 242 " pdb=" CA LEUAP 242 " pdb=" CB LEUAP 242 " pdb=" CG LEUAP 242 " ideal model delta sinusoidal sigma weight residual -180.00 -127.04 -52.96 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" N LEUAL 242 " pdb=" CA LEUAL 242 " pdb=" CB LEUAL 242 " pdb=" CG LEUAL 242 " ideal model delta sinusoidal sigma weight residual -180.00 -127.06 -52.94 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" N LEUAM 242 " pdb=" CA LEUAM 242 " pdb=" CB LEUAM 242 " pdb=" CG LEUAM 242 " ideal model delta sinusoidal sigma weight residual -180.00 -127.06 -52.94 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2346 0.025 - 0.051: 1217 0.051 - 0.076: 378 0.076 - 0.101: 245 0.101 - 0.126: 110 Chirality restraints: 4296 Sorted by residual: chirality pdb=" CA VALAM 114 " pdb=" N VALAM 114 " pdb=" C VALAM 114 " pdb=" CB VALAM 114 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VALAK 114 " pdb=" N VALAK 114 " pdb=" C VALAK 114 " pdb=" CB VALAK 114 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VALAO 114 " pdb=" N VALAO 114 " pdb=" C VALAO 114 " pdb=" CB VALAO 114 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 4293 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGAP 209 " -0.192 9.50e-02 1.11e+02 8.70e-02 6.14e+00 pdb=" NE ARGAP 209 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARGAP 209 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARGAP 209 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARGAP 209 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGAO 209 " -0.193 9.50e-02 1.11e+02 8.71e-02 6.13e+00 pdb=" NE ARGAO 209 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARGAO 209 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARGAO 209 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARGAO 209 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGAJ 209 " -0.193 9.50e-02 1.11e+02 8.71e-02 6.13e+00 pdb=" NE ARGAJ 209 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARGAJ 209 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARGAJ 209 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARGAJ 209 " 0.000 2.00e-02 2.50e+03 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 164 2.61 - 3.18: 22277 3.18 - 3.75: 36367 3.75 - 4.33: 49743 4.33 - 4.90: 87822 Nonbonded interactions: 196373 Sorted by model distance: nonbonded pdb=" OG SERAG 102 " pdb=" OD1 ASPAK 149 " model vdw 2.032 3.040 nonbonded pdb=" OD1 ASPAM 149 " pdb=" OG SERAO 102 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASPAG 149 " pdb=" OG SERAI 102 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASPAI 149 " pdb=" OG SERAK 102 " model vdw 2.237 3.040 nonbonded pdb=" NH2 ARGAM 90 " pdb=" OG1 THRAM 230 " model vdw 2.257 3.120 ... (remaining 196368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 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 : 0.002 0.018 28440 Z= 0.098 Angle : 0.428 3.951 38748 Z= 0.222 Chirality : 0.040 0.126 4296 Planarity : 0.005 0.087 5136 Dihedral : 7.616 55.689 10476 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.58 % Allowed : 1.98 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 3528 helix: 2.12 (0.21), residues: 672 sheet: 0.53 (0.19), residues: 564 loop : -1.23 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARGAP 209 TYR 0.008 0.001 TYRAG 273 PHE 0.006 0.001 PHEAJ 224 TRP 0.007 0.001 TRPAJ 140 HIS 0.003 0.001 HISAQ 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (28440) covalent geometry : angle 0.42818 / 0.22 (38748) hydrogen bonds : bond 0.27298 / 18.41 ( 815) hydrogen bonds : angle 6.31494 / 4.36 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: AH 176 MET cc_start: 0.9317 (mtt) cc_final: 0.9056 (mtt) REVERT: AI 176 MET cc_start: 0.9451 (mtt) cc_final: 0.9151 (mtm) REVERT: AJ 21 MET cc_start: 0.8872 (mtp) cc_final: 0.8580 (mtm) REVERT: AK 176 MET cc_start: 0.9415 (mtt) cc_final: 0.9158 (mtt) REVERT: AL 176 MET cc_start: 0.9429 (mtt) cc_final: 0.9097 (mtm) REVERT: AL 197 MET cc_start: 0.9215 (mtt) cc_final: 0.8641 (mtt) REVERT: AL 245 MET cc_start: 0.9295 (mtt) cc_final: 0.9071 (mtt) REVERT: AM 242 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9261 (tt) REVERT: AP 242 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9231 (tt) outliers start: 48 outliers final: 27 residues processed: 262 average time/residue: 0.1929 time to fit residues: 78.3136 Evaluate side-chains 183 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 13 VAL Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AG residue 242 LEU Chi-restraints excluded: chain AG residue 271 VAL Chi-restraints excluded: chain AH residue 13 VAL Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 242 LEU Chi-restraints excluded: chain AI residue 242 LEU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AK residue 242 LEU Chi-restraints excluded: chain AK residue 271 VAL Chi-restraints excluded: chain AL residue 242 LEU Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 242 LEU Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AN residue 242 LEU Chi-restraints excluded: chain AO residue 13 VAL Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 242 LEU Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AQ residue 242 LEU Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AM 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 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 = 0.2589 r_free = 0.2589 target = 0.049606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.040873 restraints weight = 80656.344| |-----------------------------------------------------------------------------| r_work (start): 0.2370 rms_B_bonded: 3.05 r_work: 0.2236 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 28440 Z= 0.295 Angle : 0.647 7.632 38748 Z= 0.347 Chirality : 0.046 0.138 4296 Planarity : 0.005 0.043 5136 Dihedral : 5.640 55.323 3928 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.25 % Allowed : 5.01 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3528 helix: 1.37 (0.21), residues: 708 sheet: 0.77 (0.20), residues: 564 loop : -1.32 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAJ 118 TYR 0.014 0.002 TYRAP 232 PHE 0.022 0.002 PHEAQ 237 TRP 0.015 0.003 TRPAG 192 HIS 0.005 0.002 HISAJ 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.30 (28440) covalent geometry : angle 0.64679 / 0.35 (38748) hydrogen bonds : bond 0.06322 / 4.27 ( 815) hydrogen bonds : angle 4.93809 / 3.40 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AH 176 MET cc_start: 0.9241 (mtt) cc_final: 0.9040 (mtt) REVERT: AI 10 GLU cc_start: 0.8998 (mp0) cc_final: 0.8726 (mt-10) REVERT: AJ 270 LYS cc_start: 0.9544 (mmtt) cc_final: 0.9266 (mmtt) REVERT: AN 270 LYS cc_start: 0.9386 (mmtm) cc_final: 0.8998 (mptt) REVERT: AO 186 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9210 (mtpp) REVERT: AP 154 MET cc_start: 0.8225 (mmm) cc_final: 0.7984 (mmt) REVERT: AP 197 MET cc_start: 0.9470 (mtp) cc_final: 0.9041 (mtp) REVERT: AQ 154 MET cc_start: 0.7828 (mmm) cc_final: 0.7368 (mmt) REVERT: AR 50 MET cc_start: 0.9261 (ptm) cc_final: 0.8948 (ttp) outliers start: 38 outliers final: 24 residues processed: 190 average time/residue: 0.1916 time to fit residues: 56.5663 Evaluate side-chains 178 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 13 VAL Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AG residue 271 VAL Chi-restraints excluded: chain AH residue 13 VAL Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AJ residue 36 ILE Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AK residue 271 VAL Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 36 ILE Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 13 VAL Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [2, 129, 28, 54, 282, 65, 101, 240, 103, 214, 208] chunk 2 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AM 44 ASN ** AM 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 184 GLN AQ 44 ASN ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.052338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.043899 restraints weight = 77680.859| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 3.01 r_work: 0.2303 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 28440 Z= 0.113 Angle : 0.498 6.854 38748 Z= 0.261 Chirality : 0.041 0.127 4296 Planarity : 0.004 0.026 5136 Dihedral : 4.597 56.085 3906 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.02 % Allowed : 5.63 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3528 helix: 1.49 (0.21), residues: 708 sheet: 0.85 (0.20), residues: 564 loop : -1.27 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAP 118 TYR 0.008 0.001 TYRAM 273 PHE 0.010 0.001 PHEAO 51 TRP 0.012 0.002 TRPAG 192 HIS 0.003 0.001 HISAR 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (28440) covalent geometry : angle 0.49799 / 0.26 (38748) hydrogen bonds : bond 0.04145 / 2.79 ( 815) hydrogen bonds : angle 4.60792 / 3.18 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.147 Fit side-chains REVERT: AH 176 MET cc_start: 0.9156 (mtt) cc_final: 0.8810 (mtt) REVERT: AK 10 GLU cc_start: 0.8990 (mp0) cc_final: 0.8504 (mt-10) REVERT: AL 10 GLU cc_start: 0.9012 (mp0) cc_final: 0.8752 (mt-10) REVERT: AO 186 LYS cc_start: 0.9392 (mtpp) cc_final: 0.9154 (mtpp) REVERT: AO 242 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8997 (tt) REVERT: AP 154 MET cc_start: 0.8257 (mmm) cc_final: 0.8011 (mmt) REVERT: AR 50 MET cc_start: 0.9255 (ptm) cc_final: 0.8984 (ttp) outliers start: 31 outliers final: 23 residues processed: 186 average time/residue: 0.2011 time to fit residues: 58.0470 Evaluate side-chains 177 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AG residue 271 VAL Chi-restraints excluded: chain AH residue 13 VAL Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AK residue 271 VAL Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 13 VAL Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [21, 33, 202, 107, 66, 108, 267, 326, 139, 196, 260] chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 chunk 202 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN AK 290 GLN AM 184 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.052653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.043821 restraints weight = 78840.554| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 3.06 r_work: 0.2305 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28440 Z= 0.113 Angle : 0.490 6.181 38748 Z= 0.254 Chirality : 0.041 0.128 4296 Planarity : 0.004 0.027 5136 Dihedral : 4.405 56.553 3905 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.52 % Allowed : 5.83 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3528 helix: 1.60 (0.21), residues: 708 sheet: 0.95 (0.20), residues: 564 loop : -1.25 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAH 172 TYR 0.008 0.001 TYRAO 273 PHE 0.009 0.001 PHEAO 51 TRP 0.011 0.001 TRPAG 192 HIS 0.002 0.001 HISAK 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (28440) covalent geometry : angle 0.48994 / 0.25 (38748) hydrogen bonds : bond 0.03853 / 2.59 ( 815) hydrogen bonds : angle 4.54485 / 3.15 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.030 Fit side-chains REVERT: AG 10 GLU cc_start: 0.8951 (mp0) cc_final: 0.8738 (mt-10) REVERT: AK 90 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7923 (ptm160) REVERT: AM 90 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: AN 90 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8029 (ptm160) REVERT: AO 186 LYS cc_start: 0.9379 (mtpp) cc_final: 0.9156 (mtpp) REVERT: AO 242 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8963 (tt) REVERT: AP 154 MET cc_start: 0.8268 (mmm) cc_final: 0.8018 (mmt) REVERT: AQ 90 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7764 (ptm160) REVERT: AR 50 MET cc_start: 0.9277 (ptm) cc_final: 0.8954 (ttp) outliers start: 46 outliers final: 25 residues processed: 196 average time/residue: 0.2181 time to fit residues: 64.6781 Evaluate side-chains 182 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AG residue 271 VAL Chi-restraints excluded: chain AH residue 13 VAL Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AJ residue 36 ILE Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 90 ARG Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AK residue 271 VAL Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 36 ILE Chi-restraints excluded: chain AM residue 90 ARG Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AN residue 90 ARG Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 13 VAL Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 36 ILE Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AQ residue 90 ARG Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [49, 155, 38, 235, 124, 333, 111, 176, 264, 185, 143] chunk 49 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 333 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 264 optimal weight: 0.0060 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 0.0670 overall best weight: 1.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.053443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.044623 restraints weight = 78249.304| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 3.05 r_work: 0.2325 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28440 Z= 0.092 Angle : 0.475 7.831 38748 Z= 0.244 Chirality : 0.041 0.128 4296 Planarity : 0.003 0.027 5136 Dihedral : 4.232 56.802 3905 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.52 % Allowed : 5.93 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3528 helix: 1.65 (0.21), residues: 708 sheet: 1.05 (0.20), residues: 564 loop : -1.21 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAH 90 TYR 0.008 0.001 TYRAP 273 PHE 0.009 0.001 PHEAO 51 TRP 0.012 0.001 TRPAI 205 HIS 0.002 0.001 HISAR 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 (28440) covalent geometry : angle 0.47454 / 0.24 (38748) hydrogen bonds : bond 0.03368 / 2.27 ( 815) hydrogen bonds : angle 4.48261 / 3.11 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.886 Fit side-chains REVERT: AI 176 MET cc_start: 0.9397 (mtt) cc_final: 0.9036 (mtm) REVERT: AK 10 GLU cc_start: 0.8897 (mp0) cc_final: 0.8363 (mt-10) REVERT: AK 90 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7834 (ptm160) REVERT: AL 10 GLU cc_start: 0.8942 (mp0) cc_final: 0.8684 (mt-10) REVERT: AM 154 MET cc_start: 0.8024 (mmm) cc_final: 0.7700 (mmt) REVERT: AO 186 LYS cc_start: 0.9369 (mtpp) cc_final: 0.9149 (mtpp) REVERT: AO 242 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8909 (tt) REVERT: AP 90 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7508 (ptm160) REVERT: AP 154 MET cc_start: 0.8278 (mmm) cc_final: 0.8030 (mmt) REVERT: AR 50 MET cc_start: 0.9253 (ptm) cc_final: 0.8952 (ttp) outliers start: 46 outliers final: 28 residues processed: 197 average time/residue: 0.2129 time to fit residues: 63.1917 Evaluate side-chains 185 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 13 VAL Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AJ residue 36 ILE Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 90 ARG Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AK residue 271 VAL Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 36 ILE Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AN residue 36 ILE Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 90 ARG Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 36 ILE Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [134, 306, 212, 169, 99, 13, 173, 156, 286, 192, 341] chunk 134 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 341 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.053325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.044536 restraints weight = 78504.594| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 3.06 r_work: 0.2330 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28440 Z= 0.090 Angle : 0.473 9.102 38748 Z= 0.241 Chirality : 0.041 0.129 4296 Planarity : 0.003 0.027 5136 Dihedral : 4.015 53.640 3903 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.32 % Allowed : 6.23 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 3528 helix: 1.71 (0.21), residues: 708 sheet: 1.12 (0.20), residues: 564 loop : -1.17 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAH 90 TYR 0.008 0.001 TYRAP 273 PHE 0.009 0.001 PHEAP 224 TRP 0.011 0.001 TRPAL 205 HIS 0.002 0.001 HISAR 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (28440) covalent geometry : angle 0.47301 / 0.24 (38748) hydrogen bonds : bond 0.03265 / 2.20 ( 815) hydrogen bonds : angle 4.45784 / 3.09 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.159 Fit side-chains REVERT: AG 10 GLU cc_start: 0.8878 (mp0) cc_final: 0.8670 (mt-10) REVERT: AK 10 GLU cc_start: 0.8895 (mp0) cc_final: 0.8306 (mt-10) REVERT: AL 10 GLU cc_start: 0.8938 (mp0) cc_final: 0.8671 (mt-10) REVERT: AL 176 MET cc_start: 0.9292 (mtm) cc_final: 0.9053 (mtm) REVERT: AM 154 MET cc_start: 0.7580 (mmm) cc_final: 0.7279 (mmt) REVERT: AN 270 LYS cc_start: 0.9440 (mptt) cc_final: 0.9201 (mptt) REVERT: AO 186 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9181 (mtpp) REVERT: AO 242 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8939 (tt) REVERT: AP 154 MET cc_start: 0.8365 (mmm) cc_final: 0.8102 (mmt) REVERT: AR 50 MET cc_start: 0.9222 (ptm) cc_final: 0.8913 (ttp) outliers start: 40 outliers final: 29 residues processed: 191 average time/residue: 0.1988 time to fit residues: 58.7782 Evaluate side-chains 182 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 154 MET Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AI residue 292 VAL Chi-restraints excluded: chain AJ residue 36 ILE Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 292 VAL Chi-restraints excluded: chain AN residue 36 ILE Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 36 ILE Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [111, 155, 99, 121, 15, 49, 270, 80, 135, 26, 267] chunk 111 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 15 optimal weight: 0.0030 chunk 49 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 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 = 0.2686 r_free = 0.2686 target = 0.053539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.044644 restraints weight = 78931.204| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 3.05 r_work: 0.2328 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28440 Z= 0.098 Angle : 0.478 10.697 38748 Z= 0.244 Chirality : 0.041 0.134 4296 Planarity : 0.003 0.027 5136 Dihedral : 3.898 29.392 3901 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.19 % Allowed : 6.65 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3528 helix: 1.73 (0.21), residues: 708 sheet: 1.11 (0.20), residues: 564 loop : -1.15 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAH 90 TYR 0.008 0.001 TYRAP 273 PHE 0.009 0.001 PHEAP 224 TRP 0.010 0.001 TRPAL 205 HIS 0.002 0.001 HISAR 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (28440) covalent geometry : angle 0.47754 / 0.24 (38748) hydrogen bonds : bond 0.03436 / 2.31 ( 815) hydrogen bonds : angle 4.47869 / 3.10 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.999 Fit side-chains REVERT: AH 10 GLU cc_start: 0.8963 (mp0) cc_final: 0.8535 (mt-10) REVERT: AL 10 GLU cc_start: 0.8905 (mp0) cc_final: 0.8663 (mt-10) REVERT: AL 176 MET cc_start: 0.9234 (mtm) cc_final: 0.9031 (mtm) REVERT: AM 154 MET cc_start: 0.7608 (mmm) cc_final: 0.7312 (mmt) REVERT: AO 242 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.8988 (tt) REVERT: AP 154 MET cc_start: 0.8323 (mmm) cc_final: 0.8060 (mmt) REVERT: AR 50 MET cc_start: 0.9219 (ptm) cc_final: 0.8872 (ttp) outliers start: 36 outliers final: 30 residues processed: 185 average time/residue: 0.1965 time to fit residues: 56.8149 Evaluate side-chains 186 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 154 MET Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AI residue 292 VAL Chi-restraints excluded: chain AJ residue 36 ILE Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 292 VAL Chi-restraints excluded: chain AN residue 36 ILE Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 36 ILE Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 36 ILE Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [136, 267, 63, 5, 330, 129, 141, 302, 306, 9, 124] chunk 136 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 306 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN AK 290 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 184 GLN AQ 29 GLN ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.052440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.043535 restraints weight = 79728.599| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 3.05 r_work: 0.2300 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28440 Z= 0.128 Angle : 0.505 11.775 38748 Z= 0.260 Chirality : 0.041 0.137 4296 Planarity : 0.004 0.028 5136 Dihedral : 4.032 30.789 3901 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.25 % Allowed : 6.79 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3528 helix: 1.71 (0.21), residues: 708 sheet: 1.05 (0.20), residues: 564 loop : -1.18 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAO 2 TYR 0.009 0.001 TYRAP 273 PHE 0.009 0.001 PHEAO 51 TRP 0.010 0.002 TRPAL 205 HIS 0.002 0.001 HISAK 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (28440) covalent geometry : angle 0.50516 / 0.26 (38748) hydrogen bonds : bond 0.03986 / 2.68 ( 815) hydrogen bonds : angle 4.54018 / 3.14 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.042 Fit side-chains REVERT: AI 176 MET cc_start: 0.9291 (mtt) cc_final: 0.8776 (mtm) REVERT: AK 10 GLU cc_start: 0.8931 (mp0) cc_final: 0.8503 (mt-10) REVERT: AM 154 MET cc_start: 0.7634 (mmm) cc_final: 0.7334 (mmt) REVERT: AN 270 LYS cc_start: 0.9439 (mptt) cc_final: 0.9208 (mptt) REVERT: AO 242 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.8987 (tt) REVERT: AP 154 MET cc_start: 0.8215 (mmm) cc_final: 0.7924 (mmt) REVERT: AR 50 MET cc_start: 0.9236 (ptm) cc_final: 0.8889 (ttp) outliers start: 38 outliers final: 31 residues processed: 188 average time/residue: 0.2003 time to fit residues: 58.8216 Evaluate side-chains 185 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AI residue 292 VAL Chi-restraints excluded: chain AJ residue 110 GLU Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 13 VAL Chi-restraints excluded: chain AK residue 36 ILE Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AL residue 292 VAL Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 13 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 292 VAL Chi-restraints excluded: chain AN residue 36 ILE Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 36 ILE Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 36 ILE Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [82, 27, 296, 257, 167, 331, 117, 123, 206, 108, 151] chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 331 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 108 optimal weight: 0.0010 chunk 151 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN AI 290 GLN AJ 290 GLN AK 290 GLN AL 290 GLN AM 29 GLN AN 29 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 44 ASN ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.055298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.046841 restraints weight = 76986.200| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 2.99 r_work: 0.2380 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28440 Z= 0.070 Angle : 0.465 12.288 38748 Z= 0.233 Chirality : 0.040 0.128 4296 Planarity : 0.003 0.026 5136 Dihedral : 3.701 27.408 3901 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.92 % Allowed : 7.21 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3528 helix: 2.52 (0.21), residues: 636 sheet: 1.51 (0.18), residues: 660 loop : -0.94 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAG 2 TYR 0.006 0.001 TYRAM 273 PHE 0.007 0.001 PHEAI 51 TRP 0.010 0.001 TRPAQ 192 HIS 0.001 0.000 HISAQ 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.07 (28440) covalent geometry : angle 0.46503 / 0.23 (38748) hydrogen bonds : bond 0.02455 / 1.65 ( 815) hydrogen bonds : angle 4.41534 / 3.06 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.831 Fit side-chains REVERT: AG 270 LYS cc_start: 0.9292 (mmtt) cc_final: 0.9068 (mmtt) REVERT: AI 176 MET cc_start: 0.9254 (mtt) cc_final: 0.8917 (mtm) REVERT: AK 10 GLU cc_start: 0.8935 (mp0) cc_final: 0.8505 (mt-10) REVERT: AL 10 GLU cc_start: 0.9017 (mp0) cc_final: 0.8746 (mt-10) REVERT: AM 154 MET cc_start: 0.7700 (mmm) cc_final: 0.7389 (mmt) REVERT: AO 242 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.8982 (tt) REVERT: AP 154 MET cc_start: 0.8112 (mmm) cc_final: 0.7818 (mmt) REVERT: AQ 154 MET cc_start: 0.7550 (mmm) cc_final: 0.6992 (mmp) REVERT: AQ 176 MET cc_start: 0.9193 (mtt) cc_final: 0.8877 (mtm) REVERT: AR 50 MET cc_start: 0.9212 (ptm) cc_final: 0.8834 (ttp) outliers start: 28 outliers final: 24 residues processed: 183 average time/residue: 0.1988 time to fit residues: 56.6438 Evaluate side-chains 178 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 154 MET Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AI residue 292 VAL Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AL residue 292 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 292 VAL Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [140, 318, 295, 67, 253, 192, 221, 16, 201, 228, 338] chunk 140 optimal weight: 0.0870 chunk 318 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN AI 290 GLN AJ 290 GLN AK 290 GLN AL 290 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.052429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.043673 restraints weight = 78963.581| |-----------------------------------------------------------------------------| r_work (start): 0.2442 rms_B_bonded: 3.03 r_work: 0.2310 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28440 Z= 0.131 Angle : 0.512 12.650 38748 Z= 0.261 Chirality : 0.041 0.163 4296 Planarity : 0.004 0.028 5136 Dihedral : 3.875 29.729 3899 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.89 % Allowed : 7.51 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3528 helix: 1.80 (0.21), residues: 708 sheet: 1.10 (0.20), residues: 564 loop : -1.14 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAP 2 TYR 0.009 0.001 TYRAN 273 PHE 0.009 0.001 PHEAO 51 TRP 0.010 0.002 TRPAL 205 HIS 0.003 0.001 HISAK 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (28440) covalent geometry : angle 0.51198 / 0.26 (38748) hydrogen bonds : bond 0.03948 / 2.67 ( 815) hydrogen bonds : angle 4.49906 / 3.11 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.101 Fit side-chains REVERT: AH 10 GLU cc_start: 0.9032 (mp0) cc_final: 0.8501 (mt-10) REVERT: AI 176 MET cc_start: 0.9248 (mtt) cc_final: 0.8865 (mtm) REVERT: AK 10 GLU cc_start: 0.8995 (mp0) cc_final: 0.8514 (mt-10) REVERT: AK 270 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8803 (mmmt) REVERT: AL 10 GLU cc_start: 0.8969 (mp0) cc_final: 0.8688 (mt-10) REVERT: AM 154 MET cc_start: 0.7739 (mmm) cc_final: 0.7419 (mmt) REVERT: AO 242 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.8965 (tt) REVERT: AP 154 MET cc_start: 0.8151 (mmm) cc_final: 0.7847 (mmt) REVERT: AR 50 MET cc_start: 0.9217 (ptm) cc_final: 0.8903 (ttp) outliers start: 27 outliers final: 25 residues processed: 176 average time/residue: 0.2042 time to fit residues: 55.5229 Evaluate side-chains 179 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AG residue 230 THR Chi-restraints excluded: chain AH residue 154 MET Chi-restraints excluded: chain AH residue 230 THR Chi-restraints excluded: chain AH residue 270 LYS Chi-restraints excluded: chain AI residue 230 THR Chi-restraints excluded: chain AI residue 292 VAL Chi-restraints excluded: chain AJ residue 230 THR Chi-restraints excluded: chain AK residue 154 MET Chi-restraints excluded: chain AK residue 230 THR Chi-restraints excluded: chain AL residue 230 THR Chi-restraints excluded: chain AL residue 292 VAL Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AM residue 230 THR Chi-restraints excluded: chain AM residue 292 VAL Chi-restraints excluded: chain AN residue 230 THR Chi-restraints excluded: chain AO residue 230 THR Chi-restraints excluded: chain AO residue 242 LEU Chi-restraints excluded: chain AO residue 292 VAL Chi-restraints excluded: chain AP residue 13 VAL Chi-restraints excluded: chain AP residue 110 GLU Chi-restraints excluded: chain AP residue 230 THR Chi-restraints excluded: chain AP residue 292 VAL Chi-restraints excluded: chain AQ residue 230 THR Chi-restraints excluded: chain AR residue 230 THR Chi-restraints excluded: chain AR residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [60, 252, 260, 287, 183, 39, 250, 206, 108, 315, 248] chunk 60 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 260 optimal weight: 0.5980 chunk 287 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 chunk 248 optimal weight: 0.0670 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AG 290 GLN AI 290 GLN AJ 290 GLN AK 290 GLN AL 290 GLN ** AN 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.055536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.046650 restraints weight = 78361.155| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.06 r_work: 0.2400 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28440 Z= 0.073 Angle : 0.474 12.560 38748 Z= 0.236 Chirality : 0.040 0.128 4296 Planarity : 0.003 0.026 5136 Dihedral : 3.649 27.420 3899 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.96 % Allowed : 7.51 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3528 helix: 2.53 (0.21), residues: 636 sheet: 1.50 (0.18), residues: 660 loop : -0.91 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAH 90 TYR 0.006 0.001 TYRAP 273 PHE 0.007 0.001 PHEAI 51 TRP 0.009 0.001 TRPAJ 192 HIS 0.001 0.000 HISAM 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.07 (28440) covalent geometry : angle 0.47391 / 0.24 (38748) hydrogen bonds : bond 0.02536 / 1.71 ( 815) hydrogen bonds : angle 4.38558 / 3.03 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.44 seconds wall clock time: 75 minutes 45.66 seconds (4545.66 seconds total)