Starting phenix.real_space_refine on Sun Feb 8 04:26:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.map" model { file = "/net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lah_62928/02_2026/9lah_62928.cif" } resolution = 3.16 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= 0.001 sd= 0.002 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 160 5.16 5 C 23760 2.51 5 N 7280 2.21 5 O 8260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39460 Number of models: 1 Model: "" Number of chains: 20 Chain: "Ao" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AJ" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AK" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AA" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AL" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AB" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AC" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AD" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AM" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AG" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AI" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AE" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AN" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AO" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AP" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AQ" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AR" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AH" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AF" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Chain: "AS" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1973 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 1, 'TRANS': 268} Time building chain proxies: 9.40, per 1000 atoms: 0.24 Number of scatterers: 39460 At special positions: 0 Unit cell: (134.46, 135.29, 253.98, 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 160 16.00 O 8260 8.00 N 7280 7.00 C 23760 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: 3.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10120 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 74.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'Ao' and resid 8 through 35 Processing helix chain 'Ao' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAo 84 " --> pdb=" O GLYAo 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAo 100 " --> pdb=" O THRAo 96 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 105 through 127 Processing helix chain 'Ao' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAo 191 " --> pdb=" O LEUAo 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAo 194 " --> pdb=" O ILEAo 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAo 232 " --> pdb=" O ALAAo 228 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 236 through 262 Processing helix chain 'Ao' and resid 263 through 265 No H-bonds generated for 'chain 'Ao' and resid 263 through 265' Processing helix chain 'Ao' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAo 270 " --> pdb=" O GLNAo 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAo 271 " --> pdb=" O VALAo 267 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 8 through 35 Processing helix chain 'AJ' and resid 44 through 100 removed outlier: 3.643A pdb=" N GLUAJ 84 " --> pdb=" O GLYAJ 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLUAJ 100 " --> pdb=" O THRAJ 96 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 105 through 127 Processing helix chain 'AJ' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAJ 191 " --> pdb=" O LEUAJ 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAJ 194 " --> pdb=" O ILEAJ 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAJ 232 " --> pdb=" O ALAAJ 228 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 236 through 262 Processing helix chain 'AJ' and resid 263 through 265 No H-bonds generated for 'chain 'AJ' and resid 263 through 265' Processing helix chain 'AJ' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAJ 270 " --> pdb=" O GLNAJ 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAJ 271 " --> pdb=" O VALAJ 267 " (cutoff:3.500A) Processing helix chain 'AK' and resid 8 through 35 Processing helix chain 'AK' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAK 84 " --> pdb=" O GLYAK 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) Processing helix chain 'AK' and resid 105 through 127 Processing helix chain 'AK' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAK 191 " --> pdb=" O LEUAK 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILEAK 194 " --> pdb=" O ILEAK 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAK 232 " --> pdb=" O ALAAK 228 " (cutoff:3.500A) Processing helix chain 'AK' and resid 236 through 262 Processing helix chain 'AK' and resid 263 through 265 No H-bonds generated for 'chain 'AK' and resid 263 through 265' Processing helix chain 'AK' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAK 270 " --> pdb=" O GLNAK 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAK 271 " --> pdb=" O VALAK 267 " (cutoff:3.500A) Processing helix chain 'AA' and resid 8 through 35 Processing helix chain 'AA' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAA 84 " --> pdb=" O GLYAA 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAA 100 " --> pdb=" O THRAA 96 " (cutoff:3.500A) Processing helix chain 'AA' and resid 105 through 127 Processing helix chain 'AA' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAA 191 " --> pdb=" O LEUAA 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAA 194 " --> pdb=" O ILEAA 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAA 232 " --> pdb=" O ALAAA 228 " (cutoff:3.500A) Processing helix chain 'AA' and resid 236 through 262 Processing helix chain 'AA' and resid 263 through 265 No H-bonds generated for 'chain 'AA' and resid 263 through 265' Processing helix chain 'AA' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAA 270 " --> pdb=" O GLNAA 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAA 271 " --> pdb=" O VALAA 267 " (cutoff:3.500A) Processing helix chain 'AL' and resid 8 through 35 Processing helix chain 'AL' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAL 84 " --> pdb=" O GLYAL 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAL 100 " --> pdb=" O THRAL 96 " (cutoff:3.500A) Processing helix chain 'AL' and resid 105 through 127 Processing helix chain 'AL' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAL 191 " --> pdb=" O LEUAL 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAL 194 " --> pdb=" O ILEAL 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILEAL 232 " --> pdb=" O ALAAL 228 " (cutoff:3.500A) Processing helix chain 'AL' and resid 236 through 262 Processing helix chain 'AL' and resid 263 through 265 No H-bonds generated for 'chain 'AL' and resid 263 through 265' Processing helix chain 'AL' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAL 270 " --> pdb=" O GLNAL 266 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEUAL 271 " --> pdb=" O VALAL 267 " (cutoff:3.500A) Processing helix chain 'AB' and resid 8 through 35 Processing helix chain 'AB' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAB 84 " --> pdb=" O GLYAB 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAB 100 " --> pdb=" O THRAB 96 " (cutoff:3.500A) Processing helix chain 'AB' and resid 105 through 127 Processing helix chain 'AB' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAB 191 " --> pdb=" O LEUAB 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAB 194 " --> pdb=" O ILEAB 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAB 232 " --> pdb=" O ALAAB 228 " (cutoff:3.500A) Processing helix chain 'AB' and resid 236 through 262 Processing helix chain 'AB' and resid 263 through 265 No H-bonds generated for 'chain 'AB' and resid 263 through 265' Processing helix chain 'AB' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAB 270 " --> pdb=" O GLNAB 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAB 271 " --> pdb=" O VALAB 267 " (cutoff:3.500A) Processing helix chain 'AC' and resid 8 through 35 Processing helix chain 'AC' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAC 84 " --> pdb=" O GLYAC 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAC 100 " --> pdb=" O THRAC 96 " (cutoff:3.500A) Processing helix chain 'AC' and resid 105 through 127 Processing helix chain 'AC' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAC 191 " --> pdb=" O LEUAC 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAC 194 " --> pdb=" O ILEAC 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAC 232 " --> pdb=" O ALAAC 228 " (cutoff:3.500A) Processing helix chain 'AC' and resid 236 through 262 Processing helix chain 'AC' and resid 263 through 265 No H-bonds generated for 'chain 'AC' and resid 263 through 265' Processing helix chain 'AC' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAC 270 " --> pdb=" O GLNAC 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAC 271 " --> pdb=" O VALAC 267 " (cutoff:3.500A) Processing helix chain 'AD' and resid 8 through 35 Processing helix chain 'AD' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAD 84 " --> pdb=" O GLYAD 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAD 100 " --> pdb=" O THRAD 96 " (cutoff:3.500A) Processing helix chain 'AD' and resid 105 through 127 Processing helix chain 'AD' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAD 191 " --> pdb=" O LEUAD 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAD 194 " --> pdb=" O ILEAD 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAD 232 " --> pdb=" O ALAAD 228 " (cutoff:3.500A) Processing helix chain 'AD' and resid 236 through 262 Processing helix chain 'AD' and resid 263 through 265 No H-bonds generated for 'chain 'AD' and resid 263 through 265' Processing helix chain 'AD' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAD 270 " --> pdb=" O GLNAD 266 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUAD 271 " --> pdb=" O VALAD 267 " (cutoff:3.500A) Processing helix chain 'AM' and resid 8 through 35 Processing helix chain 'AM' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAM 84 " --> pdb=" O GLYAM 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAM 100 " --> pdb=" O THRAM 96 " (cutoff:3.500A) Processing helix chain 'AM' and resid 105 through 127 Processing helix chain 'AM' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAM 191 " --> pdb=" O LEUAM 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAM 194 " --> pdb=" O ILEAM 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAM 232 " --> pdb=" O ALAAM 228 " (cutoff:3.500A) Processing helix chain 'AM' and resid 236 through 262 Processing helix chain 'AM' and resid 263 through 265 No H-bonds generated for 'chain 'AM' and resid 263 through 265' Processing helix chain 'AM' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAM 270 " --> pdb=" O GLNAM 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAM 271 " --> pdb=" O VALAM 267 " (cutoff:3.500A) Processing helix chain 'AG' and resid 8 through 35 Processing helix chain 'AG' and resid 44 through 100 removed outlier: 3.643A pdb=" N GLUAG 84 " --> pdb=" O GLYAG 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAG 100 " --> pdb=" O THRAG 96 " (cutoff:3.500A) Processing helix chain 'AG' and resid 105 through 127 Processing helix chain 'AG' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAG 191 " --> pdb=" O LEUAG 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAG 194 " --> pdb=" O ILEAG 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAG 232 " --> pdb=" O ALAAG 228 " (cutoff:3.500A) Processing helix chain 'AG' and resid 236 through 262 Processing helix chain 'AG' and resid 263 through 265 No H-bonds generated for 'chain 'AG' and resid 263 through 265' Processing helix chain 'AG' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAG 270 " --> pdb=" O GLNAG 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAG 271 " --> pdb=" O VALAG 267 " (cutoff:3.500A) Processing helix chain 'AI' and resid 8 through 35 Processing helix chain 'AI' and resid 44 through 100 removed outlier: 3.643A pdb=" N GLUAI 84 " --> pdb=" O GLYAI 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAI 100 " --> pdb=" O THRAI 96 " (cutoff:3.500A) Processing helix chain 'AI' and resid 105 through 127 Processing helix chain 'AI' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAI 191 " --> pdb=" O LEUAI 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILEAI 194 " --> pdb=" O ILEAI 190 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILEAI 232 " --> pdb=" O ALAAI 228 " (cutoff:3.500A) Processing helix chain 'AI' and resid 236 through 262 Processing helix chain 'AI' and resid 263 through 265 No H-bonds generated for 'chain 'AI' and resid 263 through 265' Processing helix chain 'AI' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAI 270 " --> pdb=" O GLNAI 266 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEUAI 271 " --> pdb=" O VALAI 267 " (cutoff:3.500A) Processing helix chain 'AE' and resid 8 through 35 Processing helix chain 'AE' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAE 84 " --> pdb=" O GLYAE 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAE 100 " --> pdb=" O THRAE 96 " (cutoff:3.500A) Processing helix chain 'AE' and resid 105 through 127 Processing helix chain 'AE' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAE 191 " --> pdb=" O LEUAE 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILEAE 194 " --> pdb=" O ILEAE 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILEAE 232 " --> pdb=" O ALAAE 228 " (cutoff:3.500A) Processing helix chain 'AE' and resid 236 through 262 Processing helix chain 'AE' and resid 263 through 265 No H-bonds generated for 'chain 'AE' and resid 263 through 265' Processing helix chain 'AE' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAE 270 " --> pdb=" O GLNAE 266 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEUAE 271 " --> pdb=" O VALAE 267 " (cutoff:3.500A) Processing helix chain 'AN' and resid 8 through 35 Processing helix chain 'AN' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAN 84 " --> pdb=" O GLYAN 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAN 100 " --> pdb=" O THRAN 96 " (cutoff:3.500A) Processing helix chain 'AN' and resid 105 through 127 Processing helix chain 'AN' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAN 191 " --> pdb=" O LEUAN 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAN 194 " --> pdb=" O ILEAN 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAN 232 " --> pdb=" O ALAAN 228 " (cutoff:3.500A) Processing helix chain 'AN' and resid 236 through 262 Processing helix chain 'AN' and resid 263 through 265 No H-bonds generated for 'chain 'AN' and resid 263 through 265' Processing helix chain 'AN' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAN 270 " --> pdb=" O GLNAN 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAN 271 " --> pdb=" O VALAN 267 " (cutoff:3.500A) Processing helix chain 'AO' and resid 8 through 35 Processing helix chain 'AO' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAO 84 " --> pdb=" O GLYAO 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAO 100 " --> pdb=" O THRAO 96 " (cutoff:3.500A) Processing helix chain 'AO' and resid 105 through 127 Processing helix chain 'AO' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAO 191 " --> pdb=" O LEUAO 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAO 194 " --> pdb=" O ILEAO 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILEAO 232 " --> pdb=" O ALAAO 228 " (cutoff:3.500A) Processing helix chain 'AO' and resid 236 through 262 Processing helix chain 'AO' and resid 263 through 265 No H-bonds generated for 'chain 'AO' and resid 263 through 265' Processing helix chain 'AO' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAO 270 " --> pdb=" O GLNAO 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAO 271 " --> pdb=" O VALAO 267 " (cutoff:3.500A) Processing helix chain 'AP' and resid 8 through 35 Processing helix chain 'AP' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAP 84 " --> pdb=" O GLYAP 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLUAP 100 " --> pdb=" O THRAP 96 " (cutoff:3.500A) Processing helix chain 'AP' and resid 105 through 127 Processing helix chain 'AP' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAP 191 " --> pdb=" O LEUAP 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAP 194 " --> pdb=" O ILEAP 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAP 232 " --> pdb=" O ALAAP 228 " (cutoff:3.500A) Processing helix chain 'AP' and resid 236 through 262 Processing helix chain 'AP' and resid 263 through 265 No H-bonds generated for 'chain 'AP' and resid 263 through 265' Processing helix chain 'AP' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAP 270 " --> pdb=" O GLNAP 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAP 271 " --> pdb=" O VALAP 267 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 8 through 35 Processing helix chain 'AQ' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAQ 84 " --> pdb=" O GLYAQ 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAQ 100 " --> pdb=" O THRAQ 96 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 105 through 127 Processing helix chain 'AQ' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAQ 191 " --> pdb=" O LEUAQ 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAQ 194 " --> pdb=" O ILEAQ 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAQ 232 " --> pdb=" O ALAAQ 228 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 236 through 262 Processing helix chain 'AQ' and resid 263 through 265 No H-bonds generated for 'chain 'AQ' and resid 263 through 265' Processing helix chain 'AQ' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAQ 270 " --> pdb=" O GLNAQ 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAQ 271 " --> pdb=" O VALAQ 267 " (cutoff:3.500A) Processing helix chain 'AR' and resid 8 through 35 Processing helix chain 'AR' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAR 84 " --> pdb=" O GLYAR 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAR 100 " --> pdb=" O THRAR 96 " (cutoff:3.500A) Processing helix chain 'AR' and resid 105 through 127 Processing helix chain 'AR' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAR 191 " --> pdb=" O LEUAR 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAR 194 " --> pdb=" O ILEAR 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAR 232 " --> pdb=" O ALAAR 228 " (cutoff:3.500A) Processing helix chain 'AR' and resid 236 through 262 Processing helix chain 'AR' and resid 263 through 265 No H-bonds generated for 'chain 'AR' and resid 263 through 265' Processing helix chain 'AR' and resid 266 through 272 removed outlier: 4.092A pdb=" N SERAR 270 " --> pdb=" O GLNAR 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAR 271 " --> pdb=" O VALAR 267 " (cutoff:3.500A) Processing helix chain 'AH' and resid 8 through 35 Processing helix chain 'AH' and resid 44 through 100 removed outlier: 3.643A pdb=" N GLUAH 84 " --> pdb=" O GLYAH 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLUAH 100 " --> pdb=" O THRAH 96 " (cutoff:3.500A) Processing helix chain 'AH' and resid 105 through 127 Processing helix chain 'AH' and resid 179 through 234 removed outlier: 3.582A pdb=" N ASPAH 191 " --> pdb=" O LEUAH 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAH 194 " --> pdb=" O ILEAH 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAH 232 " --> pdb=" O ALAAH 228 " (cutoff:3.500A) Processing helix chain 'AH' and resid 236 through 262 Processing helix chain 'AH' and resid 263 through 265 No H-bonds generated for 'chain 'AH' and resid 263 through 265' Processing helix chain 'AH' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAH 270 " --> pdb=" O GLNAH 266 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEUAH 271 " --> pdb=" O VALAH 267 " (cutoff:3.500A) Processing helix chain 'AF' and resid 8 through 35 Processing helix chain 'AF' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAF 84 " --> pdb=" O GLYAF 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLUAF 100 " --> pdb=" O THRAF 96 " (cutoff:3.500A) Processing helix chain 'AF' and resid 105 through 127 Processing helix chain 'AF' and resid 179 through 234 removed outlier: 3.581A pdb=" N ASPAF 191 " --> pdb=" O LEUAF 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAF 194 " --> pdb=" O ILEAF 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILEAF 232 " --> pdb=" O ALAAF 228 " (cutoff:3.500A) Processing helix chain 'AF' and resid 236 through 262 Processing helix chain 'AF' and resid 263 through 265 No H-bonds generated for 'chain 'AF' and resid 263 through 265' Processing helix chain 'AF' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAF 270 " --> pdb=" O GLNAF 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAF 271 " --> pdb=" O VALAF 267 " (cutoff:3.500A) Processing helix chain 'AS' and resid 8 through 35 Processing helix chain 'AS' and resid 44 through 100 removed outlier: 3.642A pdb=" N GLUAS 84 " --> pdb=" O GLYAS 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLUAS 100 " --> pdb=" O THRAS 96 " (cutoff:3.500A) Processing helix chain 'AS' and resid 105 through 127 Processing helix chain 'AS' and resid 179 through 234 removed outlier: 3.583A pdb=" N ASPAS 191 " --> pdb=" O LEUAS 187 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILEAS 194 " --> pdb=" O ILEAS 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEAS 232 " --> pdb=" O ALAAS 228 " (cutoff:3.500A) Processing helix chain 'AS' and resid 236 through 262 Processing helix chain 'AS' and resid 263 through 265 No H-bonds generated for 'chain 'AS' and resid 263 through 265' Processing helix chain 'AS' and resid 266 through 272 removed outlier: 4.093A pdb=" N SERAS 270 " --> pdb=" O GLNAS 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUAS 271 " --> pdb=" O VALAS 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ao' and resid 146 through 149 Processing sheet with id=AA2, first strand: chain 'AJ' and resid 146 through 149 Processing sheet with id=AA3, first strand: chain 'AK' and resid 146 through 149 Processing sheet with id=AA4, first strand: chain 'AA' and resid 146 through 149 Processing sheet with id=AA5, first strand: chain 'AL' and resid 146 through 149 Processing sheet with id=AA6, first strand: chain 'AB' and resid 146 through 149 Processing sheet with id=AA7, first strand: chain 'AC' and resid 146 through 149 Processing sheet with id=AA8, first strand: chain 'AD' and resid 146 through 149 Processing sheet with id=AA9, first strand: chain 'AM' and resid 146 through 149 Processing sheet with id=AB1, first strand: chain 'AG' and resid 146 through 149 Processing sheet with id=AB2, first strand: chain 'AI' and resid 146 through 149 Processing sheet with id=AB3, first strand: chain 'AE' and resid 146 through 149 Processing sheet with id=AB4, first strand: chain 'AN' and resid 146 through 149 Processing sheet with id=AB5, first strand: chain 'AO' and resid 146 through 149 Processing sheet with id=AB6, first strand: chain 'AP' and resid 146 through 149 Processing sheet with id=AB7, first strand: chain 'AQ' and resid 146 through 149 Processing sheet with id=AB8, first strand: chain 'AR' and resid 146 through 149 Processing sheet with id=AB9, first strand: chain 'AH' and resid 146 through 149 Processing sheet with id=AC1, first strand: chain 'AF' and resid 146 through 149 Processing sheet with id=AC2, first strand: chain 'AS' and resid 146 through 149 3420 hydrogen bonds defined for protein. 10200 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: 6.82 Time building geometry restraints manager: 4.91 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: 14240 1.34 - 1.46: 3086 1.46 - 1.57: 21914 1.57 - 1.69: 0 1.69 - 1.80: 320 Bond restraints: 39560 Sorted by residual: bond pdb=" CA ILEAN 38 " pdb=" CB ILEAN 38 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.47e-01 bond pdb=" CA ILEAI 38 " pdb=" CB ILEAI 38 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 8.81e-01 bond pdb=" CA ILEAE 38 " pdb=" CB ILEAE 38 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 8.64e-01 bond pdb=" CA ILEAC 38 " pdb=" CB ILEAC 38 " ideal model delta sigma weight residual 1.540 1.528 0.013 1.36e-02 5.41e+03 8.51e-01 bond pdb=" CA ILEAL 38 " pdb=" CB ILEAL 38 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 8.34e-01 ... (remaining 39555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 50678 0.94 - 1.88: 2327 1.88 - 2.82: 230 2.82 - 3.77: 45 3.77 - 4.71: 20 Bond angle restraints: 53300 Sorted by residual: angle pdb=" N THRAA 179 " pdb=" CA THRAA 179 " pdb=" C THRAA 179 " ideal model delta sigma weight residual 108.42 105.82 2.60 1.54e+00 4.22e-01 2.85e+00 angle pdb=" N THRAR 179 " pdb=" CA THRAR 179 " pdb=" C THRAR 179 " ideal model delta sigma weight residual 108.42 105.82 2.60 1.54e+00 4.22e-01 2.85e+00 angle pdb=" N THRAE 179 " pdb=" CA THRAE 179 " pdb=" C THRAE 179 " ideal model delta sigma weight residual 108.42 105.83 2.59 1.54e+00 4.22e-01 2.83e+00 angle pdb=" N THRAL 179 " pdb=" CA THRAL 179 " pdb=" C THRAL 179 " ideal model delta sigma weight residual 108.42 105.83 2.59 1.54e+00 4.22e-01 2.82e+00 angle pdb=" N THRAJ 179 " pdb=" CA THRAJ 179 " pdb=" C THRAJ 179 " ideal model delta sigma weight residual 108.42 105.84 2.58 1.54e+00 4.22e-01 2.80e+00 ... (remaining 53295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.05: 22214 12.05 - 24.10: 2053 24.10 - 36.16: 440 36.16 - 48.21: 93 48.21 - 60.26: 60 Dihedral angle restraints: 24860 sinusoidal: 9360 harmonic: 15500 Sorted by residual: dihedral pdb=" CA ASPAF 108 " pdb=" CB ASPAF 108 " pdb=" CG ASPAF 108 " pdb=" OD1 ASPAF 108 " ideal model delta sinusoidal sigma weight residual -30.00 -82.02 52.02 1 2.00e+01 2.50e-03 9.23e+00 dihedral pdb=" CA ASPAK 108 " pdb=" CB ASPAK 108 " pdb=" CG ASPAK 108 " pdb=" OD1 ASPAK 108 " ideal model delta sinusoidal sigma weight residual -30.00 -82.02 52.02 1 2.00e+01 2.50e-03 9.23e+00 dihedral pdb=" CA ASPAC 108 " pdb=" CB ASPAC 108 " pdb=" CG ASPAC 108 " pdb=" OD1 ASPAC 108 " ideal model delta sinusoidal sigma weight residual -30.00 -82.01 52.01 1 2.00e+01 2.50e-03 9.23e+00 ... (remaining 24857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4314 0.028 - 0.055: 1571 0.055 - 0.083: 515 0.083 - 0.111: 116 0.111 - 0.139: 24 Chirality restraints: 6540 Sorted by residual: chirality pdb=" CB VALAS 172 " pdb=" CA VALAS 172 " pdb=" CG1 VALAS 172 " pdb=" CG2 VALAS 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CB VALAM 172 " pdb=" CA VALAM 172 " pdb=" CG1 VALAM 172 " pdb=" CG2 VALAM 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CB VALAA 172 " pdb=" CA VALAA 172 " pdb=" CG1 VALAA 172 " pdb=" CG2 VALAA 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 6537 not shown) Planarity restraints: 7100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUAK 264 " 0.013 5.00e-02 4.00e+02 1.98e-02 6.28e-01 pdb=" N PROAK 265 " -0.034 5.00e-02 4.00e+02 pdb=" CA PROAK 265 " 0.010 5.00e-02 4.00e+02 pdb=" CD PROAK 265 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUAP 264 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.25e-01 pdb=" N PROAP 265 " 0.034 5.00e-02 4.00e+02 pdb=" CA PROAP 265 " -0.010 5.00e-02 4.00e+02 pdb=" CD PROAP 265 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUAS 264 " -0.013 5.00e-02 4.00e+02 1.97e-02 6.19e-01 pdb=" N PROAS 265 " 0.034 5.00e-02 4.00e+02 pdb=" CA PROAS 265 " -0.010 5.00e-02 4.00e+02 pdb=" CD PROAS 265 " -0.011 5.00e-02 4.00e+02 ... (remaining 7097 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8129 2.77 - 3.30: 42624 3.30 - 3.83: 65796 3.83 - 4.37: 75672 4.37 - 4.90: 131607 Nonbonded interactions: 323828 Sorted by model distance: nonbonded pdb=" O ASNAR 8 " pdb=" OG SERAR 11 " model vdw 2.233 3.040 nonbonded pdb=" O ASNAO 8 " pdb=" OG SERAO 11 " model vdw 2.234 3.040 nonbonded pdb=" O ASNAS 8 " pdb=" OG SERAS 11 " model vdw 2.234 3.040 nonbonded pdb=" O ASNAG 8 " pdb=" OG SERAG 11 " model vdw 2.234 3.040 nonbonded pdb=" O ASNAI 8 " pdb=" OG SERAI 11 " model vdw 2.234 3.040 ... (remaining 323823 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: 0.02 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = 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' selection = chain 'AS' selection = chain 'Ao' } 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: 2.360 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: 0.060 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 35.600 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 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 : 0.005 0.026 39560 Z= 0.224 Angle : 0.453 4.708 53300 Z= 0.281 Chirality : 0.033 0.139 6540 Planarity : 0.002 0.020 7100 Dihedral : 10.303 60.259 14740 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 2.44 (0.11), residues: 5360 helix: 2.78 (0.07), residues: 3900 sheet: 0.27 (0.38), residues: 240 loop : -2.27 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAC 231 PHE 0.010 0.001 PHEAI 132 HIS 0.001 0.000 HISAM 213 Details of bonding type rmsd covalent geometry : bond 0.00468 (39560) covalent geometry : angle 0.45297 (53300) hydrogen bonds : bond 0.12527 ( 3420) hydrogen bonds : angle 4.30268 (10200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9247 (mtt) cc_final: 0.7684 (mtp) REVERT: Ao 30 GLU cc_start: 0.8700 (tt0) cc_final: 0.8479 (tt0) REVERT: Ao 240 GLU cc_start: 0.8778 (tp30) cc_final: 0.8100 (tp30) REVERT: AJ 240 GLU cc_start: 0.8822 (tp30) cc_final: 0.7979 (tp30) REVERT: AJ 243 GLN cc_start: 0.9411 (mm110) cc_final: 0.9146 (mm110) REVERT: AK 29 MET cc_start: 0.9234 (mtt) cc_final: 0.8860 (mtt) REVERT: AK 30 GLU cc_start: 0.8656 (tt0) cc_final: 0.8384 (tt0) REVERT: AK 31 ARG cc_start: 0.9308 (mtt180) cc_final: 0.9107 (mtt-85) REVERT: AK 156 GLU cc_start: 0.8542 (mp0) cc_final: 0.8135 (mp0) REVERT: AK 227 ASP cc_start: 0.8854 (t0) cc_final: 0.8624 (t0) REVERT: AK 240 GLU cc_start: 0.8805 (tp30) cc_final: 0.8008 (tp30) REVERT: AK 260 GLN cc_start: 0.9221 (mt0) cc_final: 0.8888 (tm-30) REVERT: AA 29 MET cc_start: 0.9276 (mtt) cc_final: 0.7442 (mtt) REVERT: AA 156 GLU cc_start: 0.8594 (mp0) cc_final: 0.8318 (mp0) REVERT: AA 241 THR cc_start: 0.9591 (m) cc_final: 0.9344 (p) REVERT: AL 29 MET cc_start: 0.9255 (mtt) cc_final: 0.8830 (mtm) REVERT: AL 125 GLU cc_start: 0.8801 (tp30) cc_final: 0.8263 (tp30) REVERT: AL 240 GLU cc_start: 0.8734 (tp30) cc_final: 0.7561 (tp30) REVERT: AB 29 MET cc_start: 0.9209 (mtt) cc_final: 0.8768 (mtm) REVERT: AB 156 GLU cc_start: 0.8459 (mp0) cc_final: 0.7824 (mp0) REVERT: AB 231 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8204 (ttt180) REVERT: AB 240 GLU cc_start: 0.8800 (tp30) cc_final: 0.7821 (tp30) REVERT: AB 243 GLN cc_start: 0.9423 (mm110) cc_final: 0.9202 (mm110) REVERT: AC 156 GLU cc_start: 0.8538 (mp0) cc_final: 0.8135 (mp0) REVERT: AC 227 ASP cc_start: 0.8899 (t0) cc_final: 0.8640 (t0) REVERT: AC 240 GLU cc_start: 0.8848 (tp30) cc_final: 0.8573 (tp30) REVERT: AM 29 MET cc_start: 0.9253 (mtt) cc_final: 0.8421 (mtt) REVERT: AM 30 GLU cc_start: 0.8675 (tt0) cc_final: 0.8449 (tt0) REVERT: AM 156 GLU cc_start: 0.8544 (mp0) cc_final: 0.8081 (mp0) REVERT: AM 227 ASP cc_start: 0.8880 (t0) cc_final: 0.8652 (t0) REVERT: AG 29 MET cc_start: 0.9244 (mtt) cc_final: 0.8688 (mtp) REVERT: AG 227 ASP cc_start: 0.8936 (t0) cc_final: 0.8682 (t0) REVERT: AG 240 GLU cc_start: 0.8820 (tp30) cc_final: 0.7970 (tp30) REVERT: AG 244 MET cc_start: 0.9227 (ttp) cc_final: 0.9016 (ttt) REVERT: AI 30 GLU cc_start: 0.8724 (tt0) cc_final: 0.8490 (tt0) REVERT: AI 84 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8629 (mt-10) REVERT: AI 100 GLU cc_start: 0.8898 (tp30) cc_final: 0.8359 (tt0) REVERT: AI 156 GLU cc_start: 0.8624 (mp0) cc_final: 0.8047 (mp0) REVERT: AI 227 ASP cc_start: 0.8850 (t0) cc_final: 0.8635 (t0) REVERT: AI 240 GLU cc_start: 0.8813 (tp30) cc_final: 0.8574 (tp30) REVERT: AI 244 MET cc_start: 0.9191 (ttp) cc_final: 0.8980 (ttt) REVERT: AE 29 MET cc_start: 0.9222 (mtt) cc_final: 0.8847 (mtp) REVERT: AE 156 GLU cc_start: 0.8548 (mp0) cc_final: 0.8128 (mp0) REVERT: AE 227 ASP cc_start: 0.8864 (t0) cc_final: 0.8628 (t0) REVERT: AE 240 GLU cc_start: 0.8796 (tp30) cc_final: 0.8136 (tp30) REVERT: AE 244 MET cc_start: 0.9078 (ttp) cc_final: 0.8848 (ttt) REVERT: AE 260 GLN cc_start: 0.9176 (mt0) cc_final: 0.8925 (tm-30) REVERT: AN 30 GLU cc_start: 0.8739 (tt0) cc_final: 0.8521 (tt0) REVERT: AN 84 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8624 (mt-10) REVERT: AN 100 GLU cc_start: 0.8953 (tp30) cc_final: 0.8310 (tt0) REVERT: AN 156 GLU cc_start: 0.8642 (mp0) cc_final: 0.8329 (mp0) REVERT: AN 240 GLU cc_start: 0.8726 (tp30) cc_final: 0.8506 (tp30) REVERT: AN 257 MET cc_start: 0.9483 (mmm) cc_final: 0.9239 (mmm) REVERT: AO 29 MET cc_start: 0.9299 (mtt) cc_final: 0.8945 (mtp) REVERT: AO 240 GLU cc_start: 0.8748 (tp30) cc_final: 0.7473 (tp30) REVERT: AP 30 GLU cc_start: 0.8770 (tt0) cc_final: 0.8417 (tt0) REVERT: AP 84 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8672 (mt-10) REVERT: AP 100 GLU cc_start: 0.8909 (tp30) cc_final: 0.8321 (tt0) REVERT: AP 156 GLU cc_start: 0.8598 (mp0) cc_final: 0.8355 (mp0) REVERT: AP 227 ASP cc_start: 0.8857 (t0) cc_final: 0.8630 (t0) REVERT: AP 240 GLU cc_start: 0.8698 (tp30) cc_final: 0.8030 (tp30) REVERT: AP 244 MET cc_start: 0.9213 (ttp) cc_final: 0.8880 (ttt) REVERT: AQ 84 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8737 (tp30) REVERT: AQ 100 GLU cc_start: 0.8931 (tp30) cc_final: 0.8217 (tt0) REVERT: AQ 240 GLU cc_start: 0.8769 (tp30) cc_final: 0.8550 (tp30) REVERT: AR 30 GLU cc_start: 0.8691 (tt0) cc_final: 0.8415 (tt0) REVERT: AR 84 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8725 (mt-10) REVERT: AR 100 GLU cc_start: 0.8903 (tp30) cc_final: 0.8198 (tt0) REVERT: AR 156 GLU cc_start: 0.8557 (mp0) cc_final: 0.8208 (mp0) REVERT: AR 227 ASP cc_start: 0.8870 (t0) cc_final: 0.8588 (t0) REVERT: AR 244 MET cc_start: 0.9213 (ttp) cc_final: 0.8915 (ttt) REVERT: AR 260 GLN cc_start: 0.9238 (mt0) cc_final: 0.9022 (tm-30) REVERT: AH 156 GLU cc_start: 0.8484 (mp0) cc_final: 0.7996 (mp0) REVERT: AH 227 ASP cc_start: 0.8890 (t0) cc_final: 0.8682 (t0) REVERT: AH 240 GLU cc_start: 0.8797 (tp30) cc_final: 0.8306 (tp30) REVERT: AF 30 GLU cc_start: 0.8701 (tt0) cc_final: 0.8429 (tt0) REVERT: AF 84 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8742 (mt-10) REVERT: AF 100 GLU cc_start: 0.8948 (tp30) cc_final: 0.8214 (tt0) REVERT: AF 156 GLU cc_start: 0.8554 (mp0) cc_final: 0.8232 (mp0) REVERT: AF 227 ASP cc_start: 0.8860 (t0) cc_final: 0.8582 (t0) REVERT: AF 260 GLN cc_start: 0.9190 (mt0) cc_final: 0.8985 (tm-30) REVERT: AS 13 LYS cc_start: 0.9610 (mttt) cc_final: 0.9259 (pttt) REVERT: AS 29 MET cc_start: 0.9224 (mtt) cc_final: 0.8621 (mtm) REVERT: AS 156 GLU cc_start: 0.8475 (mp0) cc_final: 0.7964 (mp0) REVERT: AS 220 ASN cc_start: 0.9186 (t0) cc_final: 0.8962 (t0) REVERT: AS 240 GLU cc_start: 0.8817 (tp30) cc_final: 0.7631 (tp30) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.2705 time to fit residues: 266.5424 Evaluate side-chains 425 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ao 87 ASN Ao 247 ASN AJ 87 ASN AJ 243 GLN AJ 247 ASN AK 87 ASN AK 243 GLN AK 247 ASN AA 87 ASN AA 247 ASN AL 87 ASN AB 87 ASN AB 243 GLN AB 247 ASN AC 87 ASN AC 243 GLN AD 87 ASN AM 87 ASN AM 243 GLN AM 247 ASN AG 87 ASN AI 87 ASN AI 247 ASN AE 87 ASN AE 243 GLN AN 87 ASN AN 247 ASN AO 87 ASN AO 247 ASN AP 87 ASN AP 243 GLN AP 247 ASN AQ 87 ASN AQ 243 GLN AR 87 ASN AR 243 GLN AR 247 ASN AH 87 ASN AH 247 ASN AF 6 ASN AF 87 ASN AF 243 GLN AF 247 ASN AS 87 ASN AS 247 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.038113 restraints weight = 160312.298| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.28 r_work: 0.2551 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39560 Z= 0.203 Angle : 0.480 7.214 53300 Z= 0.263 Chirality : 0.035 0.191 6540 Planarity : 0.002 0.022 7100 Dihedral : 3.101 13.519 5600 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % 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: 3.82 (0.11), residues: 5360 helix: 3.79 (0.07), residues: 3960 sheet: 0.77 (0.42), residues: 240 loop : -2.07 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAQ 66 PHE 0.009 0.001 PHEAB 132 HIS 0.001 0.000 HISAo 213 Details of bonding type rmsd covalent geometry : bond 0.00430 (39560) covalent geometry : angle 0.47996 (53300) hydrogen bonds : bond 0.05763 ( 3420) hydrogen bonds : angle 3.18829 (10200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 487 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9463 (mtt) cc_final: 0.8338 (mtt) REVERT: Ao 240 GLU cc_start: 0.9114 (tp30) cc_final: 0.8671 (tp30) REVERT: AJ 125 GLU cc_start: 0.9357 (tp30) cc_final: 0.9110 (tp30) REVERT: AJ 156 GLU cc_start: 0.8794 (mp0) cc_final: 0.8097 (mp0) REVERT: AJ 240 GLU cc_start: 0.9156 (tp30) cc_final: 0.8394 (tp30) REVERT: AK 24 ASP cc_start: 0.8894 (t0) cc_final: 0.8527 (t0) REVERT: AK 29 MET cc_start: 0.9331 (mtt) cc_final: 0.9036 (mtt) REVERT: AK 30 GLU cc_start: 0.9113 (tt0) cc_final: 0.8860 (tt0) REVERT: AK 84 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9157 (tp30) REVERT: AK 94 ASP cc_start: 0.8392 (m-30) cc_final: 0.8146 (m-30) REVERT: AK 156 GLU cc_start: 0.8706 (mp0) cc_final: 0.8040 (mp0) REVERT: AK 240 GLU cc_start: 0.9186 (tp30) cc_final: 0.8497 (tp30) REVERT: AK 260 GLN cc_start: 0.9427 (mt0) cc_final: 0.9199 (tm-30) REVERT: AA 125 GLU cc_start: 0.9222 (tp30) cc_final: 0.8759 (tp30) REVERT: AA 156 GLU cc_start: 0.8704 (mp0) cc_final: 0.8292 (mp0) REVERT: AA 240 GLU cc_start: 0.9109 (tp30) cc_final: 0.8578 (tp30) REVERT: AA 260 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8876 (tm-30) REVERT: AL 125 GLU cc_start: 0.9245 (tp30) cc_final: 0.8690 (tp30) REVERT: AL 156 GLU cc_start: 0.8621 (mp0) cc_final: 0.8205 (mp0) REVERT: AL 240 GLU cc_start: 0.9095 (tp30) cc_final: 0.7979 (tp30) REVERT: AL 244 MET cc_start: 0.9602 (ttp) cc_final: 0.9348 (ttt) REVERT: AB 24 ASP cc_start: 0.9089 (t0) cc_final: 0.8792 (t70) REVERT: AB 29 MET cc_start: 0.9418 (mtt) cc_final: 0.9085 (mtp) REVERT: AB 88 MET cc_start: 0.9634 (mtm) cc_final: 0.8950 (mtm) REVERT: AB 156 GLU cc_start: 0.8726 (mp0) cc_final: 0.8072 (mp0) REVERT: AB 240 GLU cc_start: 0.9225 (tp30) cc_final: 0.8286 (tp30) REVERT: AC 156 GLU cc_start: 0.8784 (mp0) cc_final: 0.8119 (mp0) REVERT: AC 240 GLU cc_start: 0.9183 (tp30) cc_final: 0.8127 (tp30) REVERT: AC 260 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8716 (tm-30) REVERT: AD 156 GLU cc_start: 0.8692 (mp0) cc_final: 0.8193 (mp0) REVERT: AM 24 ASP cc_start: 0.8900 (t0) cc_final: 0.8580 (t0) REVERT: AM 29 MET cc_start: 0.9467 (mtt) cc_final: 0.9051 (mtp) REVERT: AM 30 GLU cc_start: 0.9087 (tt0) cc_final: 0.8871 (tt0) REVERT: AM 156 GLU cc_start: 0.8663 (mp0) cc_final: 0.8099 (mp0) REVERT: AM 240 GLU cc_start: 0.9114 (tp30) cc_final: 0.8706 (tp30) REVERT: AM 260 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8735 (tm-30) REVERT: AG 30 GLU cc_start: 0.9117 (tt0) cc_final: 0.8911 (tm-30) REVERT: AG 88 MET cc_start: 0.9591 (mtm) cc_final: 0.9194 (mtm) REVERT: AG 156 GLU cc_start: 0.8615 (mp0) cc_final: 0.7900 (mp0) REVERT: AG 227 ASP cc_start: 0.9342 (t0) cc_final: 0.9128 (t0) REVERT: AG 240 GLU cc_start: 0.9165 (tp30) cc_final: 0.8356 (tp30) REVERT: AG 244 MET cc_start: 0.9545 (ttp) cc_final: 0.9305 (ttt) REVERT: AI 24 ASP cc_start: 0.8834 (t0) cc_final: 0.8561 (t0) REVERT: AI 84 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8811 (mt-10) REVERT: AI 100 GLU cc_start: 0.8827 (tp30) cc_final: 0.8234 (tt0) REVERT: AI 125 GLU cc_start: 0.9027 (tp30) cc_final: 0.8775 (tp30) REVERT: AI 156 GLU cc_start: 0.8627 (mp0) cc_final: 0.8061 (mp0) REVERT: AI 240 GLU cc_start: 0.9099 (tp30) cc_final: 0.8755 (tp30) REVERT: AI 260 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8774 (tm-30) REVERT: AE 84 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8943 (tp30) REVERT: AE 156 GLU cc_start: 0.8663 (mp0) cc_final: 0.8147 (mp0) REVERT: AE 240 GLU cc_start: 0.9109 (tp30) cc_final: 0.8776 (tp30) REVERT: AE 244 MET cc_start: 0.9476 (ttp) cc_final: 0.9242 (ttt) REVERT: AE 260 GLN cc_start: 0.9335 (mt0) cc_final: 0.9005 (tm-30) REVERT: AN 30 GLU cc_start: 0.9219 (tt0) cc_final: 0.8949 (tt0) REVERT: AN 84 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8809 (mt-10) REVERT: AN 88 MET cc_start: 0.9274 (mtm) cc_final: 0.8380 (mmt) REVERT: AN 100 GLU cc_start: 0.8875 (tp30) cc_final: 0.8089 (tt0) REVERT: AN 125 GLU cc_start: 0.9150 (tp30) cc_final: 0.8895 (tp30) REVERT: AN 156 GLU cc_start: 0.8756 (mp0) cc_final: 0.8256 (mp0) REVERT: AN 240 GLU cc_start: 0.9086 (tp30) cc_final: 0.8764 (tp30) REVERT: AN 257 MET cc_start: 0.9608 (mmm) cc_final: 0.9366 (mmm) REVERT: AN 260 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8591 (tm-30) REVERT: AO 240 GLU cc_start: 0.9116 (tp30) cc_final: 0.7838 (tp30) REVERT: AO 260 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8877 (tm-30) REVERT: AP 30 GLU cc_start: 0.9258 (tt0) cc_final: 0.8905 (tt0) REVERT: AP 84 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8780 (mt-10) REVERT: AP 100 GLU cc_start: 0.8848 (tp30) cc_final: 0.8205 (tt0) REVERT: AP 156 GLU cc_start: 0.8676 (mp0) cc_final: 0.8241 (mp0) REVERT: AP 227 ASP cc_start: 0.9292 (t0) cc_final: 0.9082 (t0) REVERT: AP 240 GLU cc_start: 0.9097 (tp30) cc_final: 0.8782 (tp30) REVERT: AP 260 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8700 (tm-30) REVERT: AQ 84 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8913 (tp30) REVERT: AQ 100 GLU cc_start: 0.8930 (tp30) cc_final: 0.8151 (tt0) REVERT: AQ 156 GLU cc_start: 0.8581 (mp0) cc_final: 0.8093 (mp0) REVERT: AQ 240 GLU cc_start: 0.9152 (tp30) cc_final: 0.8804 (tp30) REVERT: AQ 260 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8766 (tm-30) REVERT: AR 30 GLU cc_start: 0.9188 (tt0) cc_final: 0.8924 (tt0) REVERT: AR 84 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8806 (mt-10) REVERT: AR 100 GLU cc_start: 0.8832 (tp30) cc_final: 0.8183 (tt0) REVERT: AR 125 GLU cc_start: 0.9208 (tp30) cc_final: 0.8939 (tp30) REVERT: AR 156 GLU cc_start: 0.8636 (mp0) cc_final: 0.8135 (mp0) REVERT: AR 227 ASP cc_start: 0.9324 (t0) cc_final: 0.9074 (t0) REVERT: AR 240 GLU cc_start: 0.9176 (tp30) cc_final: 0.8771 (tp30) REVERT: AR 244 MET cc_start: 0.9485 (ttp) cc_final: 0.9236 (ttt) REVERT: AR 260 GLN cc_start: 0.9342 (mt0) cc_final: 0.9091 (tm-30) REVERT: AH 84 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8912 (tp30) REVERT: AH 156 GLU cc_start: 0.8644 (mp0) cc_final: 0.8012 (mp0) REVERT: AH 260 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8757 (tm-30) REVERT: AF 30 GLU cc_start: 0.9181 (tt0) cc_final: 0.8976 (tt0) REVERT: AF 84 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8915 (mt-10) REVERT: AF 100 GLU cc_start: 0.8860 (tp30) cc_final: 0.8200 (tt0) REVERT: AF 125 GLU cc_start: 0.9158 (tp30) cc_final: 0.8898 (tp30) REVERT: AF 156 GLU cc_start: 0.8694 (mp0) cc_final: 0.8202 (mp0) REVERT: AF 240 GLU cc_start: 0.9164 (tp30) cc_final: 0.8776 (tp30) REVERT: AF 260 GLN cc_start: 0.9300 (mt0) cc_final: 0.9076 (tm-30) REVERT: AS 24 ASP cc_start: 0.9068 (t0) cc_final: 0.8796 (t70) REVERT: AS 125 GLU cc_start: 0.9359 (tp30) cc_final: 0.8973 (tp30) REVERT: AS 156 GLU cc_start: 0.8627 (mp0) cc_final: 0.7958 (mp0) REVERT: AS 240 GLU cc_start: 0.9200 (tp30) cc_final: 0.8746 (tp30) outliers start: 13 outliers final: 7 residues processed: 496 average time/residue: 0.2133 time to fit residues: 182.4761 Evaluate side-chains 436 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 429 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AD residue 207 ILE Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AP residue 190 ILE Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 137 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 417 optimal weight: 20.0000 chunk 399 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 504 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 366 optimal weight: 30.0000 chunk 168 optimal weight: 6.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AK 39 ASN AL 247 ASN AC 247 ASN AD 247 ASN AG 247 ASN AN 243 GLN AQ 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038896 restraints weight = 160623.196| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.30 r_work: 0.2577 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 39560 Z= 0.162 Angle : 0.419 7.246 53300 Z= 0.233 Chirality : 0.033 0.122 6540 Planarity : 0.002 0.023 7100 Dihedral : 3.015 14.864 5600 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.38 % Allowed : 7.49 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.43 (0.12), residues: 5360 helix: 4.22 (0.07), residues: 3960 sheet: 1.05 (0.42), residues: 240 loop : -1.80 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAK 66 PHE 0.008 0.001 PHEAL 132 HIS 0.001 0.000 HISAR 213 Details of bonding type rmsd covalent geometry : bond 0.00337 (39560) covalent geometry : angle 0.41939 (53300) hydrogen bonds : bond 0.05322 ( 3420) hydrogen bonds : angle 2.95126 (10200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 470 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9427 (mtt) cc_final: 0.8247 (mtt) REVERT: Ao 125 GLU cc_start: 0.9211 (tp30) cc_final: 0.8992 (tp30) REVERT: Ao 240 GLU cc_start: 0.9091 (tp30) cc_final: 0.8671 (tp30) REVERT: AJ 125 GLU cc_start: 0.9379 (tp30) cc_final: 0.9076 (tp30) REVERT: AJ 156 GLU cc_start: 0.8785 (mp0) cc_final: 0.8091 (mp0) REVERT: AJ 240 GLU cc_start: 0.9146 (tp30) cc_final: 0.8389 (tp30) REVERT: AK 24 ASP cc_start: 0.8894 (t0) cc_final: 0.8526 (t0) REVERT: AK 30 GLU cc_start: 0.9097 (tt0) cc_final: 0.8855 (tt0) REVERT: AK 84 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9117 (tp30) REVERT: AK 94 ASP cc_start: 0.8269 (m-30) cc_final: 0.8031 (m-30) REVERT: AK 100 GLU cc_start: 0.8963 (tp30) cc_final: 0.8247 (tt0) REVERT: AK 156 GLU cc_start: 0.8686 (mp0) cc_final: 0.8065 (mp0) REVERT: AK 240 GLU cc_start: 0.9150 (tp30) cc_final: 0.8441 (tp30) REVERT: AA 125 GLU cc_start: 0.9212 (tp30) cc_final: 0.8861 (tp30) REVERT: AA 156 GLU cc_start: 0.8695 (mp0) cc_final: 0.7731 (mp0) REVERT: AA 240 GLU cc_start: 0.9075 (tp30) cc_final: 0.8446 (tp30) REVERT: AA 260 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8868 (tm-30) REVERT: AL 24 ASP cc_start: 0.8916 (t0) cc_final: 0.8547 (t0) REVERT: AL 125 GLU cc_start: 0.9172 (tp30) cc_final: 0.8718 (tp30) REVERT: AL 156 GLU cc_start: 0.8596 (mp0) cc_final: 0.8099 (mp0) REVERT: AL 240 GLU cc_start: 0.9126 (tp30) cc_final: 0.7988 (tp30) REVERT: AL 244 MET cc_start: 0.9585 (ttp) cc_final: 0.9350 (ttt) REVERT: AB 24 ASP cc_start: 0.9102 (t0) cc_final: 0.8853 (t0) REVERT: AB 88 MET cc_start: 0.9602 (mtm) cc_final: 0.8977 (mtm) REVERT: AB 125 GLU cc_start: 0.9232 (tp30) cc_final: 0.8853 (tp30) REVERT: AB 156 GLU cc_start: 0.8739 (mp0) cc_final: 0.8091 (mp0) REVERT: AB 240 GLU cc_start: 0.9202 (tp30) cc_final: 0.8205 (tp30) REVERT: AC 30 GLU cc_start: 0.9259 (tt0) cc_final: 0.9033 (tm-30) REVERT: AC 84 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9090 (tp30) REVERT: AC 156 GLU cc_start: 0.8757 (mp0) cc_final: 0.8082 (mp0) REVERT: AC 240 GLU cc_start: 0.9181 (tp30) cc_final: 0.8119 (tp30) REVERT: AC 260 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8592 (tm-30) REVERT: AD 156 GLU cc_start: 0.8660 (mp0) cc_final: 0.8200 (mp0) REVERT: AD 240 GLU cc_start: 0.9121 (tp30) cc_final: 0.8037 (tp30) REVERT: AD 260 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8478 (tm-30) REVERT: AM 24 ASP cc_start: 0.8908 (t0) cc_final: 0.8552 (t0) REVERT: AM 29 MET cc_start: 0.9403 (mtt) cc_final: 0.8893 (mtt) REVERT: AM 30 GLU cc_start: 0.9086 (tt0) cc_final: 0.8886 (tt0) REVERT: AM 84 GLU cc_start: 0.9264 (mm-30) cc_final: 0.9050 (tp30) REVERT: AM 156 GLU cc_start: 0.8698 (mp0) cc_final: 0.8115 (mp0) REVERT: AM 240 GLU cc_start: 0.9098 (tp30) cc_final: 0.8638 (tp30) REVERT: AG 30 GLU cc_start: 0.9061 (tt0) cc_final: 0.8853 (tm-30) REVERT: AG 125 GLU cc_start: 0.9194 (tp30) cc_final: 0.8914 (tp30) REVERT: AG 156 GLU cc_start: 0.8554 (mp0) cc_final: 0.7852 (mp0) REVERT: AG 227 ASP cc_start: 0.9328 (t0) cc_final: 0.9097 (t0) REVERT: AG 240 GLU cc_start: 0.9165 (tp30) cc_final: 0.8313 (tp30) REVERT: AG 244 MET cc_start: 0.9538 (ttp) cc_final: 0.9302 (ttt) REVERT: AI 24 ASP cc_start: 0.8836 (t0) cc_final: 0.8514 (t0) REVERT: AI 84 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8807 (mt-10) REVERT: AI 100 GLU cc_start: 0.8759 (tp30) cc_final: 0.8190 (tt0) REVERT: AI 122 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7345 (mm-30) REVERT: AI 125 GLU cc_start: 0.9086 (tp30) cc_final: 0.8727 (tp30) REVERT: AI 156 GLU cc_start: 0.8634 (mp0) cc_final: 0.7976 (mp0) REVERT: AI 240 GLU cc_start: 0.9087 (tp30) cc_final: 0.8729 (tp30) REVERT: AI 260 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8722 (tm-30) REVERT: AE 29 MET cc_start: 0.9316 (mtp) cc_final: 0.8790 (mtp) REVERT: AE 84 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8854 (tp30) REVERT: AE 156 GLU cc_start: 0.8699 (mp0) cc_final: 0.8169 (mp0) REVERT: AE 240 GLU cc_start: 0.9079 (tp30) cc_final: 0.8740 (tp30) REVERT: AE 244 MET cc_start: 0.9476 (ttp) cc_final: 0.9262 (ttt) REVERT: AE 260 GLN cc_start: 0.9285 (mt0) cc_final: 0.9005 (tm-30) REVERT: AN 30 GLU cc_start: 0.9265 (tt0) cc_final: 0.9014 (tt0) REVERT: AN 84 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8827 (mt-10) REVERT: AN 88 MET cc_start: 0.9287 (mtm) cc_final: 0.8292 (mmt) REVERT: AN 100 GLU cc_start: 0.8799 (tp30) cc_final: 0.8093 (tt0) REVERT: AN 122 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7158 (mm-30) REVERT: AN 125 GLU cc_start: 0.9153 (tp30) cc_final: 0.8755 (tp30) REVERT: AN 156 GLU cc_start: 0.8705 (mp0) cc_final: 0.8171 (mp0) REVERT: AN 240 GLU cc_start: 0.9071 (tp30) cc_final: 0.8736 (tp30) REVERT: AN 260 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8696 (tm-30) REVERT: AO 240 GLU cc_start: 0.9106 (tp30) cc_final: 0.7799 (tp30) REVERT: AO 260 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8882 (tm-30) REVERT: AP 30 GLU cc_start: 0.9232 (tt0) cc_final: 0.8876 (tt0) REVERT: AP 84 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8710 (mt-10) REVERT: AP 100 GLU cc_start: 0.8819 (tp30) cc_final: 0.8103 (tt0) REVERT: AP 156 GLU cc_start: 0.8658 (mp0) cc_final: 0.8217 (mp0) REVERT: AP 227 ASP cc_start: 0.9258 (t0) cc_final: 0.9020 (t0) REVERT: AP 240 GLU cc_start: 0.9092 (tp30) cc_final: 0.8723 (tp30) REVERT: AP 260 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8547 (tm-30) REVERT: AQ 84 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8895 (tp30) REVERT: AQ 100 GLU cc_start: 0.8955 (tp30) cc_final: 0.8123 (tt0) REVERT: AQ 156 GLU cc_start: 0.8568 (mp0) cc_final: 0.8048 (mp0) REVERT: AQ 240 GLU cc_start: 0.9181 (tp30) cc_final: 0.8781 (tp30) REVERT: AQ 260 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8653 (tm-30) REVERT: AR 30 GLU cc_start: 0.9171 (tt0) cc_final: 0.8925 (tt0) REVERT: AR 84 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8775 (mt-10) REVERT: AR 88 MET cc_start: 0.9353 (mtm) cc_final: 0.8319 (mmt) REVERT: AR 100 GLU cc_start: 0.8818 (tp30) cc_final: 0.8160 (tt0) REVERT: AR 125 GLU cc_start: 0.9266 (tp30) cc_final: 0.8899 (tp30) REVERT: AR 156 GLU cc_start: 0.8580 (mp0) cc_final: 0.8031 (mp0) REVERT: AR 227 ASP cc_start: 0.9306 (t0) cc_final: 0.9064 (t0) REVERT: AR 240 GLU cc_start: 0.9181 (tp30) cc_final: 0.8712 (tp30) REVERT: AR 244 MET cc_start: 0.9474 (ttp) cc_final: 0.9223 (ttt) REVERT: AR 260 GLN cc_start: 0.9316 (mt0) cc_final: 0.9100 (tm-30) REVERT: AH 84 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8945 (tp30) REVERT: AH 125 GLU cc_start: 0.9079 (tp30) cc_final: 0.8862 (tp30) REVERT: AH 156 GLU cc_start: 0.8657 (mp0) cc_final: 0.8001 (mp0) REVERT: AH 240 GLU cc_start: 0.9166 (tp30) cc_final: 0.8838 (tp30) REVERT: AH 260 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8742 (tm-30) REVERT: AF 30 GLU cc_start: 0.9166 (tt0) cc_final: 0.8954 (tt0) REVERT: AF 84 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8877 (mt-10) REVERT: AF 100 GLU cc_start: 0.8904 (tp30) cc_final: 0.8243 (tt0) REVERT: AF 125 GLU cc_start: 0.9212 (tp30) cc_final: 0.8848 (tp30) REVERT: AF 156 GLU cc_start: 0.8726 (mp0) cc_final: 0.8232 (mp0) REVERT: AF 240 GLU cc_start: 0.9168 (tp30) cc_final: 0.8739 (tp30) REVERT: AS 24 ASP cc_start: 0.9036 (t0) cc_final: 0.8693 (t0) REVERT: AS 156 GLU cc_start: 0.8622 (mp0) cc_final: 0.7943 (mp0) REVERT: AS 240 GLU cc_start: 0.9180 (tp30) cc_final: 0.8700 (tp30) outliers start: 16 outliers final: 6 residues processed: 480 average time/residue: 0.1968 time to fit residues: 163.9393 Evaluate side-chains 444 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 437 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AH residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 392 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 470 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 415 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AK 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038204 restraints weight = 161385.122| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.31 r_work: 0.2551 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 39560 Z= 0.202 Angle : 0.447 10.355 53300 Z= 0.247 Chirality : 0.034 0.109 6540 Planarity : 0.002 0.023 7100 Dihedral : 3.041 15.279 5600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.45 % Allowed : 9.06 % Favored : 90.49 % 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: 4.54 (0.12), residues: 5360 helix: 4.28 (0.07), residues: 3960 sheet: 1.12 (0.42), residues: 240 loop : -1.68 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAI 66 PHE 0.008 0.001 PHEAL 132 HIS 0.001 0.000 HISAo 213 Details of bonding type rmsd covalent geometry : bond 0.00428 (39560) covalent geometry : angle 0.44690 (53300) hydrogen bonds : bond 0.05447 ( 3420) hydrogen bonds : angle 3.02373 (10200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 451 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9475 (mtt) cc_final: 0.8280 (mtt) REVERT: Ao 125 GLU cc_start: 0.9206 (tp30) cc_final: 0.8834 (tp30) REVERT: Ao 240 GLU cc_start: 0.9176 (tp30) cc_final: 0.8759 (tp30) REVERT: AJ 125 GLU cc_start: 0.9398 (tp30) cc_final: 0.9137 (tp30) REVERT: AJ 156 GLU cc_start: 0.8770 (mp0) cc_final: 0.8050 (mp0) REVERT: AJ 240 GLU cc_start: 0.9192 (tp30) cc_final: 0.8308 (tp30) REVERT: AK 24 ASP cc_start: 0.8936 (t0) cc_final: 0.8565 (t0) REVERT: AK 84 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9067 (tp30) REVERT: AK 88 MET cc_start: 0.9607 (mtm) cc_final: 0.9343 (mtm) REVERT: AK 94 ASP cc_start: 0.8352 (m-30) cc_final: 0.8075 (m-30) REVERT: AK 100 GLU cc_start: 0.8945 (tp30) cc_final: 0.8220 (tt0) REVERT: AK 156 GLU cc_start: 0.8688 (mp0) cc_final: 0.8021 (mp0) REVERT: AK 240 GLU cc_start: 0.9204 (tp30) cc_final: 0.8539 (tp30) REVERT: AA 125 GLU cc_start: 0.9234 (tp30) cc_final: 0.8927 (tp30) REVERT: AA 156 GLU cc_start: 0.8699 (mp0) cc_final: 0.7726 (mp0) REVERT: AA 240 GLU cc_start: 0.9119 (tp30) cc_final: 0.8480 (tp30) REVERT: AA 260 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8896 (tm-30) REVERT: AL 24 ASP cc_start: 0.8960 (t0) cc_final: 0.8582 (t0) REVERT: AL 125 GLU cc_start: 0.9166 (tp30) cc_final: 0.8651 (tp30) REVERT: AL 156 GLU cc_start: 0.8591 (mp0) cc_final: 0.7612 (mp0) REVERT: AL 240 GLU cc_start: 0.9186 (tp30) cc_final: 0.8019 (tp30) REVERT: AL 260 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8840 (tm-30) REVERT: AB 24 ASP cc_start: 0.9118 (t0) cc_final: 0.8820 (t0) REVERT: AB 88 MET cc_start: 0.9598 (mtm) cc_final: 0.8984 (mtm) REVERT: AB 125 GLU cc_start: 0.9209 (tp30) cc_final: 0.8876 (tp30) REVERT: AB 156 GLU cc_start: 0.8730 (mp0) cc_final: 0.8097 (mp0) REVERT: AB 240 GLU cc_start: 0.9274 (tp30) cc_final: 0.8376 (tp30) REVERT: AC 84 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9027 (tp30) REVERT: AC 156 GLU cc_start: 0.8707 (mp0) cc_final: 0.8016 (mp0) REVERT: AC 240 GLU cc_start: 0.9216 (tp30) cc_final: 0.8212 (tp30) REVERT: AC 260 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8733 (tm-30) REVERT: AD 156 GLU cc_start: 0.8668 (mp0) cc_final: 0.8194 (mp0) REVERT: AD 260 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8633 (tm-30) REVERT: AM 24 ASP cc_start: 0.8914 (t0) cc_final: 0.8599 (t0) REVERT: AM 29 MET cc_start: 0.9356 (mtt) cc_final: 0.9150 (mtp) REVERT: AM 84 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8926 (tp30) REVERT: AM 156 GLU cc_start: 0.8655 (mp0) cc_final: 0.8024 (mp0) REVERT: AM 240 GLU cc_start: 0.9131 (tp30) cc_final: 0.8668 (tp30) REVERT: AM 260 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8957 (tm-30) REVERT: AG 65 MET cc_start: 0.9378 (mtp) cc_final: 0.9142 (mtm) REVERT: AG 125 GLU cc_start: 0.9234 (tp30) cc_final: 0.8935 (tp30) REVERT: AG 156 GLU cc_start: 0.8522 (mp0) cc_final: 0.7804 (mp0) REVERT: AG 227 ASP cc_start: 0.9336 (t0) cc_final: 0.9126 (t0) REVERT: AG 240 GLU cc_start: 0.9205 (tp30) cc_final: 0.8313 (tp30) REVERT: AG 244 MET cc_start: 0.9550 (ttp) cc_final: 0.9297 (ttt) REVERT: AI 24 ASP cc_start: 0.8863 (t0) cc_final: 0.8536 (t0) REVERT: AI 84 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8849 (mt-10) REVERT: AI 100 GLU cc_start: 0.8729 (tp30) cc_final: 0.8152 (tt0) REVERT: AI 125 GLU cc_start: 0.9099 (tp30) cc_final: 0.8727 (tp30) REVERT: AI 156 GLU cc_start: 0.8668 (mp0) cc_final: 0.7979 (mp0) REVERT: AI 240 GLU cc_start: 0.9124 (tp30) cc_final: 0.8755 (tp30) REVERT: AI 260 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8738 (tm-30) REVERT: AE 29 MET cc_start: 0.9304 (mtp) cc_final: 0.8777 (mtp) REVERT: AE 84 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8794 (tp30) REVERT: AE 156 GLU cc_start: 0.8689 (mp0) cc_final: 0.8129 (mp0) REVERT: AE 240 GLU cc_start: 0.9116 (tp30) cc_final: 0.8773 (tp30) REVERT: AE 244 MET cc_start: 0.9480 (ttp) cc_final: 0.9273 (ttt) REVERT: AE 260 GLN cc_start: 0.9284 (mt0) cc_final: 0.9015 (tm-30) REVERT: AN 30 GLU cc_start: 0.9280 (tt0) cc_final: 0.9038 (tt0) REVERT: AN 62 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9142 (tm-30) REVERT: AN 84 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8808 (mt-10) REVERT: AN 88 MET cc_start: 0.9277 (mtm) cc_final: 0.8355 (mmt) REVERT: AN 100 GLU cc_start: 0.8743 (tp30) cc_final: 0.8073 (tt0) REVERT: AN 125 GLU cc_start: 0.9161 (tp30) cc_final: 0.8728 (tp30) REVERT: AN 156 GLU cc_start: 0.8672 (mp0) cc_final: 0.8094 (mp0) REVERT: AN 240 GLU cc_start: 0.9117 (tp30) cc_final: 0.8781 (tp30) REVERT: AN 260 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: AO 125 GLU cc_start: 0.9137 (tp30) cc_final: 0.8818 (tp30) REVERT: AO 240 GLU cc_start: 0.9152 (tp30) cc_final: 0.7878 (tp30) REVERT: AO 260 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8866 (tm-30) REVERT: AP 30 GLU cc_start: 0.9241 (tt0) cc_final: 0.8866 (tt0) REVERT: AP 84 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8774 (mt-10) REVERT: AP 88 MET cc_start: 0.9312 (mtm) cc_final: 0.8304 (mmt) REVERT: AP 100 GLU cc_start: 0.8791 (tp30) cc_final: 0.8077 (tt0) REVERT: AP 156 GLU cc_start: 0.8652 (mp0) cc_final: 0.8185 (mp0) REVERT: AP 227 ASP cc_start: 0.9272 (t0) cc_final: 0.9041 (t0) REVERT: AP 240 GLU cc_start: 0.9137 (tp30) cc_final: 0.8772 (tp30) REVERT: AP 260 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8677 (tm-30) REVERT: AQ 84 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8907 (tp30) REVERT: AQ 100 GLU cc_start: 0.8935 (tp30) cc_final: 0.8087 (tt0) REVERT: AQ 156 GLU cc_start: 0.8557 (mp0) cc_final: 0.7977 (mp0) REVERT: AQ 240 GLU cc_start: 0.9191 (tp30) cc_final: 0.8779 (tp30) REVERT: AQ 260 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8744 (tm-30) REVERT: AR 30 GLU cc_start: 0.9199 (tt0) cc_final: 0.8963 (tt0) REVERT: AR 84 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8769 (mt-10) REVERT: AR 100 GLU cc_start: 0.8804 (tp30) cc_final: 0.8135 (tt0) REVERT: AR 125 GLU cc_start: 0.9273 (tp30) cc_final: 0.8857 (tp30) REVERT: AR 156 GLU cc_start: 0.8620 (mp0) cc_final: 0.8066 (mp0) REVERT: AR 227 ASP cc_start: 0.9322 (t0) cc_final: 0.9077 (t0) REVERT: AR 240 GLU cc_start: 0.9165 (tp30) cc_final: 0.8715 (tp30) REVERT: AR 244 MET cc_start: 0.9501 (ttp) cc_final: 0.9260 (ttt) REVERT: AR 260 GLN cc_start: 0.9320 (mt0) cc_final: 0.9098 (tm-30) REVERT: AH 30 GLU cc_start: 0.9219 (tt0) cc_final: 0.8949 (tm-30) REVERT: AH 84 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8913 (tp30) REVERT: AH 125 GLU cc_start: 0.9131 (tp30) cc_final: 0.8888 (tp30) REVERT: AH 156 GLU cc_start: 0.8638 (mp0) cc_final: 0.7889 (mp0) REVERT: AH 240 GLU cc_start: 0.9217 (tp30) cc_final: 0.8858 (tp30) REVERT: AH 260 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: AF 30 GLU cc_start: 0.9178 (tt0) cc_final: 0.8946 (tt0) REVERT: AF 84 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8917 (mt-10) REVERT: AF 88 MET cc_start: 0.9302 (mtp) cc_final: 0.8268 (mmt) REVERT: AF 100 GLU cc_start: 0.8878 (tp30) cc_final: 0.8196 (tt0) REVERT: AF 125 GLU cc_start: 0.9214 (tp30) cc_final: 0.8866 (tp30) REVERT: AF 156 GLU cc_start: 0.8707 (mp0) cc_final: 0.8193 (mp0) REVERT: AF 240 GLU cc_start: 0.9199 (tp30) cc_final: 0.8782 (tp30) REVERT: AF 260 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8733 (tm-30) REVERT: AS 24 ASP cc_start: 0.9101 (t0) cc_final: 0.8761 (t0) REVERT: AS 29 MET cc_start: 0.9389 (mtm) cc_final: 0.9133 (mtm) REVERT: AS 156 GLU cc_start: 0.8617 (mp0) cc_final: 0.7929 (mp0) REVERT: AS 240 GLU cc_start: 0.9237 (tp30) cc_final: 0.8708 (tp30) outliers start: 19 outliers final: 9 residues processed: 463 average time/residue: 0.2166 time to fit residues: 174.2046 Evaluate side-chains 449 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 438 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AD residue 207 ILE Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AN residue 260 GLN Chi-restraints excluded: chain AH residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 427 optimal weight: 0.0970 chunk 367 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AN 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.045407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038845 restraints weight = 159790.340| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.27 r_work: 0.2578 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 39560 Z= 0.162 Angle : 0.417 11.658 53300 Z= 0.230 Chirality : 0.033 0.111 6540 Planarity : 0.002 0.024 7100 Dihedral : 3.013 15.522 5600 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.33 % Allowed : 10.38 % Favored : 89.30 % 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: 4.65 (0.12), residues: 5360 helix: 4.37 (0.07), residues: 3960 sheet: 1.12 (0.42), residues: 240 loop : -1.69 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAI 66 PHE 0.008 0.001 PHEAB 132 HIS 0.001 0.000 HISAo 213 Details of bonding type rmsd covalent geometry : bond 0.00339 (39560) covalent geometry : angle 0.41658 (53300) hydrogen bonds : bond 0.05213 ( 3420) hydrogen bonds : angle 2.90242 (10200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 462 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9455 (mtt) cc_final: 0.8271 (mtt) REVERT: Ao 125 GLU cc_start: 0.9196 (tp30) cc_final: 0.8791 (tp30) REVERT: Ao 240 GLU cc_start: 0.9157 (tp30) cc_final: 0.8749 (tp30) REVERT: AJ 125 GLU cc_start: 0.9399 (tp30) cc_final: 0.9145 (tp30) REVERT: AJ 156 GLU cc_start: 0.8783 (mp0) cc_final: 0.8059 (mp0) REVERT: AJ 240 GLU cc_start: 0.9187 (tp30) cc_final: 0.8272 (tp30) REVERT: AK 24 ASP cc_start: 0.8901 (t0) cc_final: 0.8516 (t0) REVERT: AK 84 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9045 (tp30) REVERT: AK 94 ASP cc_start: 0.8219 (m-30) cc_final: 0.7983 (m-30) REVERT: AK 100 GLU cc_start: 0.8932 (tp30) cc_final: 0.8213 (tt0) REVERT: AK 156 GLU cc_start: 0.8680 (mp0) cc_final: 0.7961 (mp0) REVERT: AK 240 GLU cc_start: 0.9180 (tp30) cc_final: 0.8524 (tp30) REVERT: AA 125 GLU cc_start: 0.9228 (tp30) cc_final: 0.8780 (tp30) REVERT: AA 156 GLU cc_start: 0.8664 (mp0) cc_final: 0.7677 (mp0) REVERT: AA 240 GLU cc_start: 0.9075 (tp30) cc_final: 0.8339 (tp30) REVERT: AA 260 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8835 (tm-30) REVERT: AL 24 ASP cc_start: 0.8943 (t0) cc_final: 0.8553 (t0) REVERT: AL 125 GLU cc_start: 0.9150 (tp30) cc_final: 0.8635 (tp30) REVERT: AL 156 GLU cc_start: 0.8609 (mp0) cc_final: 0.7629 (mp0) REVERT: AL 240 GLU cc_start: 0.9165 (tp30) cc_final: 0.8020 (tp30) REVERT: AL 244 MET cc_start: 0.9601 (ttp) cc_final: 0.9341 (ttt) REVERT: AL 260 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8702 (tm-30) REVERT: AB 24 ASP cc_start: 0.9067 (t0) cc_final: 0.8732 (t0) REVERT: AB 29 MET cc_start: 0.9395 (mtp) cc_final: 0.9177 (mtm) REVERT: AB 88 MET cc_start: 0.9571 (mtm) cc_final: 0.8993 (mtm) REVERT: AB 125 GLU cc_start: 0.9217 (tp30) cc_final: 0.8861 (tp30) REVERT: AB 156 GLU cc_start: 0.8741 (mp0) cc_final: 0.8074 (mp0) REVERT: AB 240 GLU cc_start: 0.9253 (tp30) cc_final: 0.8244 (tp30) REVERT: AC 30 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8922 (tm-30) REVERT: AC 84 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9028 (tp30) REVERT: AC 94 ASP cc_start: 0.8187 (m-30) cc_final: 0.7958 (m-30) REVERT: AC 156 GLU cc_start: 0.8707 (mp0) cc_final: 0.7997 (mp0) REVERT: AC 240 GLU cc_start: 0.9213 (tp30) cc_final: 0.8199 (tp30) REVERT: AC 260 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8819 (tm-30) REVERT: AD 156 GLU cc_start: 0.8610 (mp0) cc_final: 0.8163 (mp0) REVERT: AD 240 GLU cc_start: 0.9164 (tp30) cc_final: 0.8061 (tp30) REVERT: AD 260 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8643 (tm-30) REVERT: AM 24 ASP cc_start: 0.8888 (t0) cc_final: 0.8559 (t0) REVERT: AM 29 MET cc_start: 0.9323 (mtt) cc_final: 0.9096 (mtt) REVERT: AM 84 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8903 (tp30) REVERT: AM 156 GLU cc_start: 0.8648 (mp0) cc_final: 0.8021 (mp0) REVERT: AM 240 GLU cc_start: 0.9106 (tp30) cc_final: 0.8645 (tp30) REVERT: AM 260 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8902 (tm-30) REVERT: AG 65 MET cc_start: 0.9409 (mtp) cc_final: 0.9207 (mtm) REVERT: AG 125 GLU cc_start: 0.9206 (tp30) cc_final: 0.8919 (tp30) REVERT: AG 156 GLU cc_start: 0.8461 (mp0) cc_final: 0.7739 (mp0) REVERT: AG 227 ASP cc_start: 0.9329 (t0) cc_final: 0.9089 (t0) REVERT: AG 240 GLU cc_start: 0.9212 (tp30) cc_final: 0.8318 (tp30) REVERT: AG 244 MET cc_start: 0.9538 (ttp) cc_final: 0.9264 (ttt) REVERT: AI 24 ASP cc_start: 0.8859 (t0) cc_final: 0.8515 (t0) REVERT: AI 84 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8819 (mt-10) REVERT: AI 100 GLU cc_start: 0.8711 (tp30) cc_final: 0.8140 (tt0) REVERT: AI 125 GLU cc_start: 0.9123 (tp30) cc_final: 0.8766 (tp30) REVERT: AI 156 GLU cc_start: 0.8630 (mp0) cc_final: 0.7986 (mp0) REVERT: AI 240 GLU cc_start: 0.9103 (tp30) cc_final: 0.8736 (tp30) REVERT: AI 260 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8667 (tm-30) REVERT: AE 29 MET cc_start: 0.9265 (mtp) cc_final: 0.8693 (mtp) REVERT: AE 84 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8758 (tp30) REVERT: AE 94 ASP cc_start: 0.8345 (m-30) cc_final: 0.8115 (m-30) REVERT: AE 100 GLU cc_start: 0.9039 (tp30) cc_final: 0.8282 (tt0) REVERT: AE 156 GLU cc_start: 0.8667 (mp0) cc_final: 0.8032 (mp0) REVERT: AE 240 GLU cc_start: 0.9086 (tp30) cc_final: 0.8730 (tp30) REVERT: AE 244 MET cc_start: 0.9469 (ttp) cc_final: 0.9254 (ttt) REVERT: AE 260 GLN cc_start: 0.9258 (mt0) cc_final: 0.9015 (tm-30) REVERT: AN 30 GLU cc_start: 0.9271 (tt0) cc_final: 0.9026 (tt0) REVERT: AN 84 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8794 (mt-10) REVERT: AN 88 MET cc_start: 0.9407 (mtm) cc_final: 0.8458 (mmt) REVERT: AN 100 GLU cc_start: 0.8741 (tp30) cc_final: 0.8067 (tt0) REVERT: AN 122 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7269 (mm-30) REVERT: AN 125 GLU cc_start: 0.9169 (tp30) cc_final: 0.8719 (tp30) REVERT: AN 156 GLU cc_start: 0.8652 (mp0) cc_final: 0.8065 (mp0) REVERT: AN 240 GLU cc_start: 0.9095 (tp30) cc_final: 0.8747 (tp30) REVERT: AN 260 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8901 (tm-30) REVERT: AO 30 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8911 (tm-30) REVERT: AO 125 GLU cc_start: 0.9146 (tp30) cc_final: 0.8810 (tp30) REVERT: AO 240 GLU cc_start: 0.9136 (tp30) cc_final: 0.8649 (tp30) REVERT: AO 260 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8866 (tm-30) REVERT: AP 30 GLU cc_start: 0.9226 (tt0) cc_final: 0.8852 (tt0) REVERT: AP 84 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8747 (mt-10) REVERT: AP 88 MET cc_start: 0.9309 (mtm) cc_final: 0.8355 (mmt) REVERT: AP 100 GLU cc_start: 0.8762 (tp30) cc_final: 0.8063 (tt0) REVERT: AP 156 GLU cc_start: 0.8630 (mp0) cc_final: 0.8128 (mp0) REVERT: AP 227 ASP cc_start: 0.9263 (t0) cc_final: 0.9025 (t0) REVERT: AP 240 GLU cc_start: 0.9111 (tp30) cc_final: 0.8739 (tp30) REVERT: AP 260 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8159 (tm-30) REVERT: AQ 84 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8873 (tp30) REVERT: AQ 100 GLU cc_start: 0.8949 (tp30) cc_final: 0.8122 (tt0) REVERT: AQ 125 GLU cc_start: 0.9157 (tp30) cc_final: 0.8920 (tp30) REVERT: AQ 156 GLU cc_start: 0.8543 (mp0) cc_final: 0.7954 (mp0) REVERT: AQ 260 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8743 (tm-30) REVERT: AR 30 GLU cc_start: 0.9187 (tt0) cc_final: 0.8937 (tt0) REVERT: AR 84 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8770 (mt-10) REVERT: AR 88 MET cc_start: 0.9328 (mtm) cc_final: 0.8254 (mmt) REVERT: AR 100 GLU cc_start: 0.8800 (tp30) cc_final: 0.8146 (tt0) REVERT: AR 125 GLU cc_start: 0.9253 (tp30) cc_final: 0.8799 (tp30) REVERT: AR 156 GLU cc_start: 0.8567 (mp0) cc_final: 0.8043 (mp0) REVERT: AR 227 ASP cc_start: 0.9310 (t0) cc_final: 0.9067 (t0) REVERT: AR 240 GLU cc_start: 0.9164 (tp30) cc_final: 0.8696 (tp30) REVERT: AR 244 MET cc_start: 0.9492 (ttp) cc_final: 0.9245 (ttt) REVERT: AR 260 GLN cc_start: 0.9289 (mt0) cc_final: 0.9084 (tm-30) REVERT: AH 84 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8872 (tp30) REVERT: AH 125 GLU cc_start: 0.9115 (tp30) cc_final: 0.8825 (tp30) REVERT: AH 156 GLU cc_start: 0.8643 (mp0) cc_final: 0.7907 (mp0) REVERT: AH 240 GLU cc_start: 0.9188 (tp30) cc_final: 0.8822 (tp30) REVERT: AH 260 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8826 (tm-30) REVERT: AF 30 GLU cc_start: 0.9182 (tt0) cc_final: 0.8948 (tt0) REVERT: AF 84 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8893 (mt-10) REVERT: AF 88 MET cc_start: 0.9296 (mtp) cc_final: 0.8269 (mmt) REVERT: AF 100 GLU cc_start: 0.8843 (tp30) cc_final: 0.8170 (tt0) REVERT: AF 125 GLU cc_start: 0.9224 (tp30) cc_final: 0.8865 (tp30) REVERT: AF 156 GLU cc_start: 0.8716 (mp0) cc_final: 0.8211 (mp0) REVERT: AF 240 GLU cc_start: 0.9160 (tp30) cc_final: 0.8732 (tp30) REVERT: AF 260 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8584 (tm-30) REVERT: AS 24 ASP cc_start: 0.9081 (t0) cc_final: 0.8725 (t0) REVERT: AS 29 MET cc_start: 0.9390 (mtm) cc_final: 0.9107 (mtm) REVERT: AS 125 GLU cc_start: 0.9346 (tp30) cc_final: 0.8947 (tp30) REVERT: AS 156 GLU cc_start: 0.8625 (mp0) cc_final: 0.7932 (mp0) REVERT: AS 240 GLU cc_start: 0.9198 (tp30) cc_final: 0.8659 (tp30) outliers start: 14 outliers final: 9 residues processed: 471 average time/residue: 0.2173 time to fit residues: 176.7699 Evaluate side-chains 462 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 451 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AN residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 425 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 463 optimal weight: 30.0000 chunk 404 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038858 restraints weight = 160519.332| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.27 r_work: 0.2577 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39560 Z= 0.161 Angle : 0.420 10.788 53300 Z= 0.231 Chirality : 0.033 0.112 6540 Planarity : 0.002 0.025 7100 Dihedral : 3.007 16.798 5600 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.33 % Allowed : 11.08 % Favored : 88.59 % 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: 4.70 (0.12), residues: 5360 helix: 4.39 (0.07), residues: 3960 sheet: 1.15 (0.42), residues: 240 loop : -1.61 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAQ 31 PHE 0.008 0.001 PHEAL 132 HIS 0.001 0.000 HISAR 213 Details of bonding type rmsd covalent geometry : bond 0.00337 (39560) covalent geometry : angle 0.42002 (53300) hydrogen bonds : bond 0.05165 ( 3420) hydrogen bonds : angle 2.88711 (10200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 464 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9455 (mtt) cc_final: 0.8316 (mtt) REVERT: Ao 125 GLU cc_start: 0.9207 (tp30) cc_final: 0.8758 (tp30) REVERT: Ao 240 GLU cc_start: 0.9172 (tp30) cc_final: 0.8766 (tp30) REVERT: AJ 156 GLU cc_start: 0.8744 (mp0) cc_final: 0.8022 (mp0) REVERT: AJ 240 GLU cc_start: 0.9204 (tp30) cc_final: 0.8310 (tp30) REVERT: AK 24 ASP cc_start: 0.8930 (t0) cc_final: 0.8578 (t0) REVERT: AK 84 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9053 (tp30) REVERT: AK 88 MET cc_start: 0.9608 (mtm) cc_final: 0.9390 (mtm) REVERT: AK 94 ASP cc_start: 0.8212 (m-30) cc_final: 0.7974 (m-30) REVERT: AK 100 GLU cc_start: 0.8913 (tp30) cc_final: 0.8197 (tt0) REVERT: AK 156 GLU cc_start: 0.8657 (mp0) cc_final: 0.7924 (mp0) REVERT: AK 240 GLU cc_start: 0.9194 (tp30) cc_final: 0.8579 (tp30) REVERT: AK 260 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8630 (tm-30) REVERT: AA 125 GLU cc_start: 0.9247 (tp30) cc_final: 0.8872 (tp30) REVERT: AA 156 GLU cc_start: 0.8674 (mp0) cc_final: 0.7659 (mp0) REVERT: AA 240 GLU cc_start: 0.9087 (tp30) cc_final: 0.8338 (tp30) REVERT: AA 260 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8839 (tm-30) REVERT: AL 24 ASP cc_start: 0.8963 (t0) cc_final: 0.8572 (t0) REVERT: AL 125 GLU cc_start: 0.9162 (tp30) cc_final: 0.8646 (tp30) REVERT: AL 156 GLU cc_start: 0.8639 (mp0) cc_final: 0.7646 (mp0) REVERT: AL 240 GLU cc_start: 0.9177 (tp30) cc_final: 0.8012 (tp30) REVERT: AL 260 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8749 (tm-30) REVERT: AB 24 ASP cc_start: 0.9073 (t0) cc_final: 0.8731 (t0) REVERT: AB 125 GLU cc_start: 0.9221 (tp30) cc_final: 0.8832 (tp30) REVERT: AB 156 GLU cc_start: 0.8754 (mp0) cc_final: 0.8086 (mp0) REVERT: AB 240 GLU cc_start: 0.9257 (tp30) cc_final: 0.8251 (tp30) REVERT: AC 30 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8938 (tm-30) REVERT: AC 84 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9028 (tp30) REVERT: AC 94 ASP cc_start: 0.8177 (m-30) cc_final: 0.7950 (m-30) REVERT: AC 156 GLU cc_start: 0.8739 (mp0) cc_final: 0.7892 (mp0) REVERT: AC 240 GLU cc_start: 0.9233 (tp30) cc_final: 0.8215 (tp30) REVERT: AC 260 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8609 (tm-30) REVERT: AD 125 GLU cc_start: 0.9407 (tp30) cc_final: 0.8979 (tp30) REVERT: AD 156 GLU cc_start: 0.8640 (mp0) cc_final: 0.8178 (mp0) REVERT: AD 260 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8686 (tm-30) REVERT: AM 24 ASP cc_start: 0.8929 (t0) cc_final: 0.8593 (t0) REVERT: AM 29 MET cc_start: 0.9366 (mtt) cc_final: 0.9085 (mtt) REVERT: AM 84 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8895 (tp30) REVERT: AM 156 GLU cc_start: 0.8625 (mp0) cc_final: 0.7993 (mp0) REVERT: AM 240 GLU cc_start: 0.9129 (tp30) cc_final: 0.8660 (tp30) REVERT: AM 260 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8921 (tm-30) REVERT: AG 156 GLU cc_start: 0.8467 (mp0) cc_final: 0.7747 (mp0) REVERT: AG 227 ASP cc_start: 0.9332 (t0) cc_final: 0.9091 (t0) REVERT: AG 240 GLU cc_start: 0.9218 (tp30) cc_final: 0.8315 (tp30) REVERT: AG 244 MET cc_start: 0.9539 (ttp) cc_final: 0.9277 (ttt) REVERT: AI 24 ASP cc_start: 0.8862 (t0) cc_final: 0.8514 (t0) REVERT: AI 84 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8833 (mt-10) REVERT: AI 100 GLU cc_start: 0.8712 (tp30) cc_final: 0.8104 (tt0) REVERT: AI 125 GLU cc_start: 0.9122 (tp30) cc_final: 0.8752 (tp30) REVERT: AI 156 GLU cc_start: 0.8615 (mp0) cc_final: 0.7947 (mp0) REVERT: AI 240 GLU cc_start: 0.9113 (tp30) cc_final: 0.8772 (tp30) REVERT: AI 260 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8669 (tm-30) REVERT: AE 29 MET cc_start: 0.9243 (mtp) cc_final: 0.8646 (mtp) REVERT: AE 84 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8787 (tp30) REVERT: AE 94 ASP cc_start: 0.8320 (m-30) cc_final: 0.8085 (m-30) REVERT: AE 100 GLU cc_start: 0.9024 (tp30) cc_final: 0.8262 (tt0) REVERT: AE 156 GLU cc_start: 0.8684 (mp0) cc_final: 0.8095 (mp0) REVERT: AE 240 GLU cc_start: 0.9088 (tp30) cc_final: 0.8724 (tp30) REVERT: AE 244 MET cc_start: 0.9473 (ttp) cc_final: 0.9256 (ttt) REVERT: AE 260 GLN cc_start: 0.9267 (mt0) cc_final: 0.9024 (tm-30) REVERT: AN 30 GLU cc_start: 0.9283 (tt0) cc_final: 0.9035 (tt0) REVERT: AN 62 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9116 (tm-30) REVERT: AN 84 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8733 (mt-10) REVERT: AN 100 GLU cc_start: 0.8731 (tp30) cc_final: 0.8038 (tt0) REVERT: AN 122 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7276 (mm-30) REVERT: AN 125 GLU cc_start: 0.9166 (tp30) cc_final: 0.8705 (tp30) REVERT: AN 156 GLU cc_start: 0.8656 (mp0) cc_final: 0.8057 (mp0) REVERT: AN 240 GLU cc_start: 0.9094 (tp30) cc_final: 0.8859 (tp30) REVERT: AN 260 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8771 (tm-30) REVERT: AO 30 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8929 (tm-30) REVERT: AO 125 GLU cc_start: 0.9151 (tp30) cc_final: 0.8750 (tp30) REVERT: AO 240 GLU cc_start: 0.9163 (tp30) cc_final: 0.8728 (tp30) REVERT: AO 260 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8858 (tm-30) REVERT: AP 30 GLU cc_start: 0.9241 (tt0) cc_final: 0.8869 (tt0) REVERT: AP 84 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8741 (mt-10) REVERT: AP 88 MET cc_start: 0.9295 (mtm) cc_final: 0.8396 (mmt) REVERT: AP 100 GLU cc_start: 0.8733 (tp30) cc_final: 0.8047 (tt0) REVERT: AP 156 GLU cc_start: 0.8620 (mp0) cc_final: 0.8105 (mp0) REVERT: AP 227 ASP cc_start: 0.9266 (t0) cc_final: 0.9017 (t0) REVERT: AP 240 GLU cc_start: 0.9109 (tp30) cc_final: 0.8735 (tp30) REVERT: AQ 84 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8840 (tp30) REVERT: AQ 100 GLU cc_start: 0.8924 (tp30) cc_final: 0.8085 (tt0) REVERT: AQ 125 GLU cc_start: 0.9150 (tp30) cc_final: 0.8905 (tp30) REVERT: AQ 156 GLU cc_start: 0.8574 (mp0) cc_final: 0.7945 (mp0) REVERT: AQ 240 GLU cc_start: 0.9214 (tp30) cc_final: 0.8789 (tp30) REVERT: AQ 260 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8687 (tm-30) REVERT: AR 30 GLU cc_start: 0.9192 (tt0) cc_final: 0.8935 (tt0) REVERT: AR 84 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8743 (mt-10) REVERT: AR 88 MET cc_start: 0.9375 (mtm) cc_final: 0.8343 (mmt) REVERT: AR 100 GLU cc_start: 0.8779 (tp30) cc_final: 0.8111 (tt0) REVERT: AR 125 GLU cc_start: 0.9253 (tp30) cc_final: 0.8781 (tp30) REVERT: AR 156 GLU cc_start: 0.8558 (mp0) cc_final: 0.8029 (mp0) REVERT: AR 227 ASP cc_start: 0.9324 (t0) cc_final: 0.9080 (t0) REVERT: AR 240 GLU cc_start: 0.9168 (tp30) cc_final: 0.8704 (tp30) REVERT: AR 244 MET cc_start: 0.9493 (ttp) cc_final: 0.9248 (ttt) REVERT: AR 260 GLN cc_start: 0.9302 (mt0) cc_final: 0.9096 (tm-30) REVERT: AH 84 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8885 (tp30) REVERT: AH 125 GLU cc_start: 0.9101 (tp30) cc_final: 0.8803 (tp30) REVERT: AH 156 GLU cc_start: 0.8637 (mp0) cc_final: 0.7910 (mp0) REVERT: AH 240 GLU cc_start: 0.9179 (tp30) cc_final: 0.8807 (tp30) REVERT: AF 30 GLU cc_start: 0.9192 (tt0) cc_final: 0.8961 (tt0) REVERT: AF 84 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8899 (mt-10) REVERT: AF 88 MET cc_start: 0.9281 (mtp) cc_final: 0.8257 (mmt) REVERT: AF 100 GLU cc_start: 0.8826 (tp30) cc_final: 0.8174 (tt0) REVERT: AF 125 GLU cc_start: 0.9224 (tp30) cc_final: 0.8866 (tp30) REVERT: AF 156 GLU cc_start: 0.8674 (mp0) cc_final: 0.8163 (mp0) REVERT: AF 240 GLU cc_start: 0.9170 (tp30) cc_final: 0.8749 (tp30) REVERT: AF 260 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8572 (tm-30) REVERT: AS 24 ASP cc_start: 0.9086 (t0) cc_final: 0.8725 (t0) REVERT: AS 29 MET cc_start: 0.9405 (mtm) cc_final: 0.9158 (mtm) REVERT: AS 125 GLU cc_start: 0.9349 (tp30) cc_final: 0.8971 (tp30) REVERT: AS 156 GLU cc_start: 0.8603 (mp0) cc_final: 0.7897 (mp0) REVERT: AS 240 GLU cc_start: 0.9208 (tp30) cc_final: 0.8667 (tp30) outliers start: 14 outliers final: 10 residues processed: 475 average time/residue: 0.2275 time to fit residues: 187.6601 Evaluate side-chains 469 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 458 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AJ residue 207 ILE Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 375 optimal weight: 0.8980 chunk 325 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 367 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 489 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AQ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.046242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.039538 restraints weight = 159305.176| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.38 r_work: 0.2599 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39560 Z= 0.131 Angle : 0.405 11.991 53300 Z= 0.221 Chirality : 0.032 0.120 6540 Planarity : 0.002 0.026 7100 Dihedral : 2.953 15.772 5600 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.35 % Allowed : 11.46 % Favored : 88.19 % 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: 4.81 (0.12), residues: 5360 helix: 4.47 (0.07), residues: 3960 sheet: 1.19 (0.42), residues: 240 loop : -1.56 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAI 66 PHE 0.007 0.001 PHEAL 132 HIS 0.001 0.000 HISAo 213 Details of bonding type rmsd covalent geometry : bond 0.00265 (39560) covalent geometry : angle 0.40463 (53300) hydrogen bonds : bond 0.04916 ( 3420) hydrogen bonds : angle 2.77917 (10200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 481 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9440 (mtt) cc_final: 0.8265 (mtt) REVERT: Ao 125 GLU cc_start: 0.9186 (tp30) cc_final: 0.8741 (tp30) REVERT: Ao 240 GLU cc_start: 0.9162 (tp30) cc_final: 0.8753 (tp30) REVERT: AJ 156 GLU cc_start: 0.8735 (mp0) cc_final: 0.8020 (mp0) REVERT: AJ 236 ASP cc_start: 0.8967 (t0) cc_final: 0.8456 (t70) REVERT: AJ 240 GLU cc_start: 0.9193 (tp30) cc_final: 0.8409 (tp30) REVERT: AK 24 ASP cc_start: 0.8928 (t0) cc_final: 0.8547 (t0) REVERT: AK 84 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9050 (tp30) REVERT: AK 94 ASP cc_start: 0.8096 (m-30) cc_final: 0.7882 (m-30) REVERT: AK 100 GLU cc_start: 0.8906 (tp30) cc_final: 0.8190 (tt0) REVERT: AK 156 GLU cc_start: 0.8659 (mp0) cc_final: 0.7936 (mp0) REVERT: AK 240 GLU cc_start: 0.9174 (tp30) cc_final: 0.8498 (tp30) REVERT: AA 125 GLU cc_start: 0.9273 (tp30) cc_final: 0.8890 (tp30) REVERT: AA 156 GLU cc_start: 0.8663 (mp0) cc_final: 0.7642 (mp0) REVERT: AA 240 GLU cc_start: 0.9085 (tp30) cc_final: 0.8270 (tp30) REVERT: AA 260 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8777 (tm-30) REVERT: AL 24 ASP cc_start: 0.8944 (t0) cc_final: 0.8566 (t0) REVERT: AL 125 GLU cc_start: 0.9123 (tp30) cc_final: 0.8610 (tp30) REVERT: AL 156 GLU cc_start: 0.8572 (mp0) cc_final: 0.7574 (mp0) REVERT: AL 240 GLU cc_start: 0.9146 (tp30) cc_final: 0.7977 (tp30) REVERT: AL 244 MET cc_start: 0.9576 (ttp) cc_final: 0.9307 (ttt) REVERT: AL 260 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8828 (tm-30) REVERT: AB 24 ASP cc_start: 0.9081 (t0) cc_final: 0.8747 (t0) REVERT: AB 125 GLU cc_start: 0.9241 (tp30) cc_final: 0.8829 (tp30) REVERT: AB 156 GLU cc_start: 0.8783 (mp0) cc_final: 0.8123 (mp0) REVERT: AB 240 GLU cc_start: 0.9252 (tp30) cc_final: 0.8218 (tp30) REVERT: AC 30 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9007 (tm-30) REVERT: AC 84 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9040 (tp30) REVERT: AC 94 ASP cc_start: 0.8121 (m-30) cc_final: 0.7905 (m-30) REVERT: AC 156 GLU cc_start: 0.8759 (mp0) cc_final: 0.7900 (mp0) REVERT: AC 240 GLU cc_start: 0.9233 (tp30) cc_final: 0.8182 (tp30) REVERT: AC 260 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8778 (tm-30) REVERT: AD 24 ASP cc_start: 0.8990 (t0) cc_final: 0.8623 (t0) REVERT: AD 30 GLU cc_start: 0.9130 (tt0) cc_final: 0.8828 (tm-30) REVERT: AD 125 GLU cc_start: 0.9380 (tp30) cc_final: 0.9003 (tp30) REVERT: AD 156 GLU cc_start: 0.8622 (mp0) cc_final: 0.8141 (mp0) REVERT: AD 240 GLU cc_start: 0.9178 (tp30) cc_final: 0.7993 (tp30) REVERT: AD 260 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8747 (tm-30) REVERT: AM 24 ASP cc_start: 0.8903 (t0) cc_final: 0.8526 (t0) REVERT: AM 29 MET cc_start: 0.9333 (mtt) cc_final: 0.9075 (mtt) REVERT: AM 84 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8938 (tp30) REVERT: AM 156 GLU cc_start: 0.8623 (mp0) cc_final: 0.7992 (mp0) REVERT: AM 240 GLU cc_start: 0.9099 (tp30) cc_final: 0.8626 (tp30) REVERT: AM 260 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8919 (tm-30) REVERT: AG 65 MET cc_start: 0.9437 (mtm) cc_final: 0.9193 (mtm) REVERT: AG 125 GLU cc_start: 0.9177 (tp30) cc_final: 0.8933 (tp30) REVERT: AG 156 GLU cc_start: 0.8447 (mp0) cc_final: 0.7731 (mp0) REVERT: AG 227 ASP cc_start: 0.9317 (t0) cc_final: 0.9097 (t0) REVERT: AG 236 ASP cc_start: 0.8926 (t0) cc_final: 0.8509 (t70) REVERT: AG 240 GLU cc_start: 0.9212 (tp30) cc_final: 0.8339 (tp30) REVERT: AG 244 MET cc_start: 0.9528 (ttp) cc_final: 0.9249 (ttt) REVERT: AI 24 ASP cc_start: 0.8854 (t0) cc_final: 0.8498 (t0) REVERT: AI 84 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8815 (mt-10) REVERT: AI 100 GLU cc_start: 0.8704 (tp30) cc_final: 0.8111 (tt0) REVERT: AI 125 GLU cc_start: 0.9135 (tp30) cc_final: 0.8761 (tp30) REVERT: AI 156 GLU cc_start: 0.8605 (mp0) cc_final: 0.7990 (mp0) REVERT: AI 240 GLU cc_start: 0.9122 (tp30) cc_final: 0.8762 (tp30) REVERT: AI 260 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8651 (tm-30) REVERT: AE 29 MET cc_start: 0.9196 (mtp) cc_final: 0.8531 (mtp) REVERT: AE 84 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8803 (tp30) REVERT: AE 94 ASP cc_start: 0.8265 (m-30) cc_final: 0.8016 (m-30) REVERT: AE 100 GLU cc_start: 0.9031 (tp30) cc_final: 0.8211 (tt0) REVERT: AE 156 GLU cc_start: 0.8691 (mp0) cc_final: 0.8094 (mp0) REVERT: AE 240 GLU cc_start: 0.9077 (tp30) cc_final: 0.8699 (tp30) REVERT: AE 244 MET cc_start: 0.9464 (ttp) cc_final: 0.9235 (ttt) REVERT: AE 260 GLN cc_start: 0.9251 (mt0) cc_final: 0.9023 (tm-30) REVERT: AN 30 GLU cc_start: 0.9263 (tt0) cc_final: 0.9014 (tt0) REVERT: AN 84 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8778 (mt-10) REVERT: AN 88 MET cc_start: 0.9050 (mtm) cc_final: 0.8073 (mmt) REVERT: AN 100 GLU cc_start: 0.8700 (tp30) cc_final: 0.8042 (tt0) REVERT: AN 122 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7288 (mm-30) REVERT: AN 125 GLU cc_start: 0.9176 (tp30) cc_final: 0.8716 (tp30) REVERT: AN 156 GLU cc_start: 0.8599 (mp0) cc_final: 0.8005 (mp0) REVERT: AN 240 GLU cc_start: 0.9105 (tp30) cc_final: 0.8865 (tp30) REVERT: AN 260 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8768 (tm-30) REVERT: AO 24 ASP cc_start: 0.8991 (t0) cc_final: 0.8667 (t0) REVERT: AO 29 MET cc_start: 0.9260 (mtp) cc_final: 0.8578 (mmm) REVERT: AO 30 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8857 (tm-30) REVERT: AO 125 GLU cc_start: 0.9154 (tp30) cc_final: 0.8747 (tp30) REVERT: AO 156 GLU cc_start: 0.8617 (mp0) cc_final: 0.7870 (mp0) REVERT: AO 240 GLU cc_start: 0.9142 (tp30) cc_final: 0.8722 (tp30) REVERT: AO 260 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8875 (tm-30) REVERT: AP 30 GLU cc_start: 0.9230 (tt0) cc_final: 0.8867 (tt0) REVERT: AP 84 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8731 (mt-10) REVERT: AP 88 MET cc_start: 0.9347 (mtm) cc_final: 0.8474 (mmt) REVERT: AP 100 GLU cc_start: 0.8771 (tp30) cc_final: 0.8047 (tt0) REVERT: AP 156 GLU cc_start: 0.8612 (mp0) cc_final: 0.8086 (mp0) REVERT: AP 227 ASP cc_start: 0.9268 (t0) cc_final: 0.9018 (t0) REVERT: AP 240 GLU cc_start: 0.9099 (tp30) cc_final: 0.8744 (tp30) REVERT: AQ 24 ASP cc_start: 0.8950 (t0) cc_final: 0.8689 (t0) REVERT: AQ 84 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8858 (tp30) REVERT: AQ 100 GLU cc_start: 0.8906 (tp30) cc_final: 0.8089 (tt0) REVERT: AQ 125 GLU cc_start: 0.9150 (tp30) cc_final: 0.8878 (tp30) REVERT: AQ 156 GLU cc_start: 0.8525 (mp0) cc_final: 0.7885 (mp0) REVERT: AQ 240 GLU cc_start: 0.9215 (tp30) cc_final: 0.8750 (tp30) REVERT: AQ 260 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8653 (tm-30) REVERT: AR 30 GLU cc_start: 0.9188 (tt0) cc_final: 0.8944 (tt0) REVERT: AR 84 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8721 (mt-10) REVERT: AR 88 MET cc_start: 0.9376 (mtm) cc_final: 0.8371 (mmt) REVERT: AR 100 GLU cc_start: 0.8796 (tp30) cc_final: 0.8114 (tt0) REVERT: AR 125 GLU cc_start: 0.9255 (tp30) cc_final: 0.8805 (tp30) REVERT: AR 156 GLU cc_start: 0.8537 (mp0) cc_final: 0.8025 (mp0) REVERT: AR 227 ASP cc_start: 0.9336 (t0) cc_final: 0.9121 (t0) REVERT: AR 240 GLU cc_start: 0.9192 (tp30) cc_final: 0.8725 (tp30) REVERT: AR 244 MET cc_start: 0.9484 (ttp) cc_final: 0.9241 (ttt) REVERT: AH 84 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8874 (tp30) REVERT: AH 100 GLU cc_start: 0.8935 (tp30) cc_final: 0.8140 (tt0) REVERT: AH 125 GLU cc_start: 0.9103 (tp30) cc_final: 0.8714 (tp30) REVERT: AH 156 GLU cc_start: 0.8628 (mp0) cc_final: 0.7898 (mp0) REVERT: AH 240 GLU cc_start: 0.9164 (tp30) cc_final: 0.8782 (tp30) REVERT: AF 30 GLU cc_start: 0.9187 (tt0) cc_final: 0.8966 (tt0) REVERT: AF 84 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8884 (mt-10) REVERT: AF 88 MET cc_start: 0.9263 (mtp) cc_final: 0.8274 (mmt) REVERT: AF 100 GLU cc_start: 0.8792 (tp30) cc_final: 0.8136 (tt0) REVERT: AF 122 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7234 (mm-30) REVERT: AF 125 GLU cc_start: 0.9245 (tp30) cc_final: 0.8878 (tp30) REVERT: AF 156 GLU cc_start: 0.8691 (mp0) cc_final: 0.8161 (mp0) REVERT: AF 240 GLU cc_start: 0.9175 (tp30) cc_final: 0.8738 (tp30) REVERT: AF 260 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: AS 24 ASP cc_start: 0.9110 (t0) cc_final: 0.8744 (t0) REVERT: AS 29 MET cc_start: 0.9407 (mtm) cc_final: 0.9050 (mtp) REVERT: AS 125 GLU cc_start: 0.9327 (tp30) cc_final: 0.8956 (tp30) REVERT: AS 156 GLU cc_start: 0.8545 (mp0) cc_final: 0.7852 (mp0) REVERT: AS 240 GLU cc_start: 0.9208 (tp30) cc_final: 0.7872 (tp30) outliers start: 15 outliers final: 9 residues processed: 490 average time/residue: 0.2250 time to fit residues: 191.1703 Evaluate side-chains 482 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 471 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AN residue 16 LYS Chi-restraints excluded: chain AH residue 272 LEU Chi-restraints excluded: chain AF residue 260 GLN Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 243 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 435 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 518 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AQ 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.039532 restraints weight = 160132.133| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.27 r_work: 0.2602 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39560 Z= 0.140 Angle : 0.421 11.197 53300 Z= 0.229 Chirality : 0.032 0.119 6540 Planarity : 0.002 0.026 7100 Dihedral : 2.950 15.613 5600 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.47 % Allowed : 12.02 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.81 (0.12), residues: 5360 helix: 4.47 (0.07), residues: 3960 sheet: 1.22 (0.42), residues: 240 loop : -1.55 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAO 231 PHE 0.007 0.001 PHEAL 132 HIS 0.001 0.000 HISAA 213 Details of bonding type rmsd covalent geometry : bond 0.00288 (39560) covalent geometry : angle 0.42149 (53300) hydrogen bonds : bond 0.04925 ( 3420) hydrogen bonds : angle 2.79282 (10200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 475 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9420 (mtt) cc_final: 0.8242 (mtt) REVERT: Ao 125 GLU cc_start: 0.9171 (tp30) cc_final: 0.8712 (tp30) REVERT: Ao 240 GLU cc_start: 0.9161 (tp30) cc_final: 0.8704 (tp30) REVERT: AJ 125 GLU cc_start: 0.9412 (tp30) cc_final: 0.8942 (tp30) REVERT: AJ 156 GLU cc_start: 0.8699 (mp0) cc_final: 0.8012 (mp0) REVERT: AJ 236 ASP cc_start: 0.8952 (t0) cc_final: 0.8461 (t70) REVERT: AJ 240 GLU cc_start: 0.9199 (tp30) cc_final: 0.8442 (tp30) REVERT: AK 24 ASP cc_start: 0.8912 (t0) cc_final: 0.8553 (t0) REVERT: AK 84 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9057 (tp30) REVERT: AK 94 ASP cc_start: 0.8099 (m-30) cc_final: 0.7888 (m-30) REVERT: AK 100 GLU cc_start: 0.8912 (tp30) cc_final: 0.8195 (tt0) REVERT: AK 156 GLU cc_start: 0.8669 (mp0) cc_final: 0.7963 (mp0) REVERT: AK 240 GLU cc_start: 0.9176 (tp30) cc_final: 0.8510 (tp30) REVERT: AA 125 GLU cc_start: 0.9248 (tp30) cc_final: 0.8831 (tp30) REVERT: AA 156 GLU cc_start: 0.8658 (mp0) cc_final: 0.7663 (mp0) REVERT: AA 240 GLU cc_start: 0.9097 (tp30) cc_final: 0.8294 (tp30) REVERT: AA 260 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8772 (tm-30) REVERT: AL 24 ASP cc_start: 0.8947 (t0) cc_final: 0.8569 (t0) REVERT: AL 125 GLU cc_start: 0.9227 (tp30) cc_final: 0.8724 (tp30) REVERT: AL 156 GLU cc_start: 0.8561 (mp0) cc_final: 0.7568 (mp0) REVERT: AL 236 ASP cc_start: 0.8993 (t0) cc_final: 0.8708 (t70) REVERT: AL 240 GLU cc_start: 0.9152 (tp30) cc_final: 0.7995 (tp30) REVERT: AL 244 MET cc_start: 0.9580 (ttp) cc_final: 0.9320 (ttt) REVERT: AL 260 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8826 (tm-30) REVERT: AB 24 ASP cc_start: 0.9070 (t0) cc_final: 0.8732 (t0) REVERT: AB 125 GLU cc_start: 0.9224 (tp30) cc_final: 0.8769 (tp30) REVERT: AB 156 GLU cc_start: 0.8794 (mp0) cc_final: 0.8148 (mp0) REVERT: AB 240 GLU cc_start: 0.9219 (tp30) cc_final: 0.8205 (tp30) REVERT: AC 30 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9027 (tm-30) REVERT: AC 84 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9015 (tp30) REVERT: AC 94 ASP cc_start: 0.8113 (m-30) cc_final: 0.7898 (m-30) REVERT: AC 156 GLU cc_start: 0.8751 (mp0) cc_final: 0.7921 (mp0) REVERT: AC 240 GLU cc_start: 0.9234 (tp30) cc_final: 0.8193 (tp30) REVERT: AC 260 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8744 (tm-30) REVERT: AD 24 ASP cc_start: 0.8970 (t0) cc_final: 0.8602 (t0) REVERT: AD 30 GLU cc_start: 0.9132 (tt0) cc_final: 0.8845 (tm-30) REVERT: AD 125 GLU cc_start: 0.9366 (tp30) cc_final: 0.8978 (tp30) REVERT: AD 156 GLU cc_start: 0.8638 (mp0) cc_final: 0.8182 (mp0) REVERT: AD 236 ASP cc_start: 0.9042 (t0) cc_final: 0.8652 (t70) REVERT: AD 240 GLU cc_start: 0.9176 (tp30) cc_final: 0.8021 (tp30) REVERT: AD 260 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8705 (tm-30) REVERT: AM 24 ASP cc_start: 0.8894 (t0) cc_final: 0.8530 (t0) REVERT: AM 29 MET cc_start: 0.9354 (mtt) cc_final: 0.9125 (mtt) REVERT: AM 84 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8938 (tp30) REVERT: AM 100 GLU cc_start: 0.8985 (tp30) cc_final: 0.8200 (tt0) REVERT: AM 156 GLU cc_start: 0.8628 (mp0) cc_final: 0.8008 (mp0) REVERT: AM 240 GLU cc_start: 0.9110 (tp30) cc_final: 0.8656 (tp30) REVERT: AM 260 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8857 (tm-30) REVERT: AG 65 MET cc_start: 0.9448 (mtm) cc_final: 0.9107 (mtm) REVERT: AG 125 GLU cc_start: 0.9155 (tp30) cc_final: 0.8830 (tp30) REVERT: AG 156 GLU cc_start: 0.8450 (mp0) cc_final: 0.7738 (mp0) REVERT: AG 227 ASP cc_start: 0.9313 (t0) cc_final: 0.9100 (t0) REVERT: AG 236 ASP cc_start: 0.8840 (t0) cc_final: 0.8433 (t70) REVERT: AG 240 GLU cc_start: 0.9205 (tp30) cc_final: 0.8343 (tp30) REVERT: AG 244 MET cc_start: 0.9530 (ttp) cc_final: 0.9251 (ttt) REVERT: AI 24 ASP cc_start: 0.8818 (t0) cc_final: 0.8476 (t0) REVERT: AI 84 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8816 (mt-10) REVERT: AI 100 GLU cc_start: 0.8717 (tp30) cc_final: 0.8131 (tt0) REVERT: AI 125 GLU cc_start: 0.9122 (tp30) cc_final: 0.8741 (tp30) REVERT: AI 156 GLU cc_start: 0.8597 (mp0) cc_final: 0.8101 (mp0) REVERT: AI 240 GLU cc_start: 0.9114 (tp30) cc_final: 0.8756 (tp30) REVERT: AI 260 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8612 (tm-30) REVERT: AE 29 MET cc_start: 0.9202 (mtp) cc_final: 0.8527 (mtp) REVERT: AE 84 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8785 (tp30) REVERT: AE 94 ASP cc_start: 0.8282 (m-30) cc_final: 0.8039 (m-30) REVERT: AE 100 GLU cc_start: 0.9036 (tp30) cc_final: 0.8218 (tt0) REVERT: AE 156 GLU cc_start: 0.8685 (mp0) cc_final: 0.8078 (mp0) REVERT: AE 240 GLU cc_start: 0.9075 (tp30) cc_final: 0.8700 (tp30) REVERT: AE 244 MET cc_start: 0.9465 (ttp) cc_final: 0.9233 (ttt) REVERT: AE 260 GLN cc_start: 0.9228 (mt0) cc_final: 0.9019 (tm-30) REVERT: AN 30 GLU cc_start: 0.9265 (tt0) cc_final: 0.9019 (tt0) REVERT: AN 84 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8784 (mt-10) REVERT: AN 88 MET cc_start: 0.9075 (mtm) cc_final: 0.8100 (mmt) REVERT: AN 100 GLU cc_start: 0.8708 (tp30) cc_final: 0.8037 (tt0) REVERT: AN 125 GLU cc_start: 0.9171 (tp30) cc_final: 0.8717 (tp30) REVERT: AN 156 GLU cc_start: 0.8596 (mp0) cc_final: 0.8057 (mp0) REVERT: AN 240 GLU cc_start: 0.9085 (tp30) cc_final: 0.8855 (tp30) REVERT: AN 260 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8793 (tm-30) REVERT: AO 24 ASP cc_start: 0.8952 (t0) cc_final: 0.8670 (t0) REVERT: AO 30 GLU cc_start: 0.9078 (tt0) cc_final: 0.8775 (tm-30) REVERT: AO 125 GLU cc_start: 0.9160 (tp30) cc_final: 0.8727 (tp30) REVERT: AO 156 GLU cc_start: 0.8630 (mp0) cc_final: 0.7895 (mp0) REVERT: AO 240 GLU cc_start: 0.9155 (tp30) cc_final: 0.7883 (tp30) REVERT: AO 260 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8855 (tm-30) REVERT: AP 30 GLU cc_start: 0.9213 (tt0) cc_final: 0.8848 (tt0) REVERT: AP 84 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8716 (mt-10) REVERT: AP 100 GLU cc_start: 0.8773 (tp30) cc_final: 0.8045 (tt0) REVERT: AP 156 GLU cc_start: 0.8613 (mp0) cc_final: 0.8098 (mp0) REVERT: AP 227 ASP cc_start: 0.9251 (t0) cc_final: 0.9007 (t0) REVERT: AP 240 GLU cc_start: 0.9086 (tp30) cc_final: 0.8741 (tp30) REVERT: AQ 84 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8850 (tp30) REVERT: AQ 100 GLU cc_start: 0.8924 (tp30) cc_final: 0.8087 (tt0) REVERT: AQ 125 GLU cc_start: 0.9155 (tp30) cc_final: 0.8867 (tp30) REVERT: AQ 156 GLU cc_start: 0.8498 (mp0) cc_final: 0.7892 (mp0) REVERT: AQ 240 GLU cc_start: 0.9229 (tp30) cc_final: 0.8785 (tp30) REVERT: AQ 260 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8577 (tm-30) REVERT: AR 30 GLU cc_start: 0.9206 (tt0) cc_final: 0.8965 (tt0) REVERT: AR 62 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8935 (mm-30) REVERT: AR 84 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8726 (mt-10) REVERT: AR 88 MET cc_start: 0.9367 (mtm) cc_final: 0.8379 (mmt) REVERT: AR 100 GLU cc_start: 0.8788 (tp30) cc_final: 0.8087 (tt0) REVERT: AR 125 GLU cc_start: 0.9257 (tp30) cc_final: 0.8804 (tp30) REVERT: AR 156 GLU cc_start: 0.8537 (mp0) cc_final: 0.8025 (mp0) REVERT: AR 227 ASP cc_start: 0.9307 (t0) cc_final: 0.9098 (t0) REVERT: AR 240 GLU cc_start: 0.9174 (tp30) cc_final: 0.8716 (tp30) REVERT: AR 244 MET cc_start: 0.9485 (ttp) cc_final: 0.9241 (ttt) REVERT: AH 84 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8863 (tp30) REVERT: AH 100 GLU cc_start: 0.8948 (tp30) cc_final: 0.8134 (tt0) REVERT: AH 125 GLU cc_start: 0.9116 (tp30) cc_final: 0.8713 (tp30) REVERT: AH 156 GLU cc_start: 0.8627 (mp0) cc_final: 0.7903 (mp0) REVERT: AH 240 GLU cc_start: 0.9169 (tp30) cc_final: 0.8785 (tp30) REVERT: AF 30 GLU cc_start: 0.9186 (tt0) cc_final: 0.8969 (tt0) REVERT: AF 84 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8889 (mt-10) REVERT: AF 88 MET cc_start: 0.9251 (mtp) cc_final: 0.8257 (mmt) REVERT: AF 100 GLU cc_start: 0.8797 (tp30) cc_final: 0.8132 (tt0) REVERT: AF 122 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7250 (mm-30) REVERT: AF 125 GLU cc_start: 0.9236 (tp30) cc_final: 0.8871 (tp30) REVERT: AF 156 GLU cc_start: 0.8643 (mp0) cc_final: 0.8121 (mp0) REVERT: AF 240 GLU cc_start: 0.9161 (tp30) cc_final: 0.8736 (tp30) REVERT: AF 260 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: AS 24 ASP cc_start: 0.9090 (t0) cc_final: 0.8718 (t0) REVERT: AS 29 MET cc_start: 0.9397 (mtm) cc_final: 0.8987 (mtp) REVERT: AS 125 GLU cc_start: 0.9305 (tp30) cc_final: 0.8921 (tp30) REVERT: AS 156 GLU cc_start: 0.8567 (mp0) cc_final: 0.7879 (mp0) REVERT: AS 240 GLU cc_start: 0.9201 (tp30) cc_final: 0.8682 (tp30) outliers start: 20 outliers final: 15 residues processed: 485 average time/residue: 0.2140 time to fit residues: 180.2142 Evaluate side-chains 485 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 468 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AJ residue 207 ILE Chi-restraints excluded: chain AJ residue 243 GLN Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AA residue 29 MET Chi-restraints excluded: chain AA residue 272 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AN residue 16 LYS Chi-restraints excluded: chain AH residue 272 LEU Chi-restraints excluded: chain AF residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 97 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 527 optimal weight: 8.9990 chunk 302 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AP 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 260 GLN AH 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.039335 restraints weight = 160772.839| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.27 r_work: 0.2596 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39560 Z= 0.148 Angle : 0.429 11.093 53300 Z= 0.232 Chirality : 0.033 0.122 6540 Planarity : 0.002 0.026 7100 Dihedral : 2.958 15.496 5600 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.47 % Allowed : 12.37 % Favored : 87.16 % 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: 4.82 (0.12), residues: 5360 helix: 4.46 (0.07), residues: 3960 sheet: 1.23 (0.42), residues: 240 loop : -1.51 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAO 231 PHE 0.008 0.001 PHEAL 132 HIS 0.001 0.000 HISAR 213 Details of bonding type rmsd covalent geometry : bond 0.00308 (39560) covalent geometry : angle 0.42853 (53300) hydrogen bonds : bond 0.04965 ( 3420) hydrogen bonds : angle 2.82418 (10200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 470 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9445 (mtt) cc_final: 0.8297 (mtt) REVERT: Ao 125 GLU cc_start: 0.9176 (tp30) cc_final: 0.8727 (tp30) REVERT: Ao 240 GLU cc_start: 0.9173 (tp30) cc_final: 0.8718 (tp30) REVERT: AJ 156 GLU cc_start: 0.8713 (mp0) cc_final: 0.8024 (mp0) REVERT: AJ 236 ASP cc_start: 0.8965 (t0) cc_final: 0.8586 (t70) REVERT: AJ 240 GLU cc_start: 0.9201 (tp30) cc_final: 0.8437 (tp30) REVERT: AJ 260 GLN cc_start: 0.9364 (tp-100) cc_final: 0.9164 (tp-100) REVERT: AK 24 ASP cc_start: 0.8922 (t0) cc_final: 0.8546 (t0) REVERT: AK 84 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9058 (tp30) REVERT: AK 94 ASP cc_start: 0.8105 (m-30) cc_final: 0.7886 (m-30) REVERT: AK 100 GLU cc_start: 0.8910 (tp30) cc_final: 0.8193 (tt0) REVERT: AK 156 GLU cc_start: 0.8661 (mp0) cc_final: 0.7946 (mp0) REVERT: AK 236 ASP cc_start: 0.8579 (t0) cc_final: 0.8083 (t0) REVERT: AK 240 GLU cc_start: 0.9197 (tp30) cc_final: 0.8552 (tp30) REVERT: AA 125 GLU cc_start: 0.9255 (tp30) cc_final: 0.8838 (tp30) REVERT: AA 156 GLU cc_start: 0.8669 (mp0) cc_final: 0.7625 (mp0) REVERT: AA 240 GLU cc_start: 0.9109 (tp30) cc_final: 0.8302 (tp30) REVERT: AA 260 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8784 (tm-30) REVERT: AL 24 ASP cc_start: 0.8940 (t0) cc_final: 0.8562 (t0) REVERT: AL 125 GLU cc_start: 0.9203 (tp30) cc_final: 0.8690 (tp30) REVERT: AL 156 GLU cc_start: 0.8564 (mp0) cc_final: 0.7571 (mp0) REVERT: AL 236 ASP cc_start: 0.8997 (t0) cc_final: 0.8710 (t70) REVERT: AL 240 GLU cc_start: 0.9162 (tp30) cc_final: 0.7971 (tp30) REVERT: AL 244 MET cc_start: 0.9583 (ttp) cc_final: 0.9323 (ttt) REVERT: AL 260 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8816 (tm-30) REVERT: AB 24 ASP cc_start: 0.9079 (t0) cc_final: 0.8743 (t0) REVERT: AB 125 GLU cc_start: 0.9232 (tp30) cc_final: 0.8774 (tp30) REVERT: AB 156 GLU cc_start: 0.8786 (mp0) cc_final: 0.8139 (mp0) REVERT: AB 240 GLU cc_start: 0.9236 (tp30) cc_final: 0.8204 (tp30) REVERT: AC 30 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9025 (tm-30) REVERT: AC 84 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9010 (tp30) REVERT: AC 94 ASP cc_start: 0.8105 (m-30) cc_final: 0.7868 (m-30) REVERT: AC 156 GLU cc_start: 0.8759 (mp0) cc_final: 0.7924 (mp0) REVERT: AC 240 GLU cc_start: 0.9239 (tp30) cc_final: 0.8198 (tp30) REVERT: AC 260 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8738 (tm-30) REVERT: AD 24 ASP cc_start: 0.8968 (t0) cc_final: 0.8599 (t0) REVERT: AD 30 GLU cc_start: 0.9139 (tt0) cc_final: 0.8848 (tm-30) REVERT: AD 125 GLU cc_start: 0.9358 (tp30) cc_final: 0.8982 (tp30) REVERT: AD 156 GLU cc_start: 0.8645 (mp0) cc_final: 0.8190 (mp0) REVERT: AD 236 ASP cc_start: 0.9042 (t0) cc_final: 0.8651 (t70) REVERT: AD 240 GLU cc_start: 0.9183 (tp30) cc_final: 0.8015 (tp30) REVERT: AD 260 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8707 (tm-30) REVERT: AM 24 ASP cc_start: 0.8900 (t0) cc_final: 0.8538 (t0) REVERT: AM 29 MET cc_start: 0.9354 (mtt) cc_final: 0.9105 (mtt) REVERT: AM 84 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8934 (tp30) REVERT: AM 100 GLU cc_start: 0.8975 (tp30) cc_final: 0.8191 (tt0) REVERT: AM 156 GLU cc_start: 0.8620 (mp0) cc_final: 0.7992 (mp0) REVERT: AM 240 GLU cc_start: 0.9124 (tp30) cc_final: 0.8677 (tp30) REVERT: AM 260 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8747 (tm-30) REVERT: AG 65 MET cc_start: 0.9459 (mtm) cc_final: 0.9085 (mtm) REVERT: AG 125 GLU cc_start: 0.9144 (tp30) cc_final: 0.8818 (tp30) REVERT: AG 156 GLU cc_start: 0.8455 (mp0) cc_final: 0.7741 (mp0) REVERT: AG 227 ASP cc_start: 0.9323 (t0) cc_final: 0.9114 (t0) REVERT: AG 236 ASP cc_start: 0.8853 (t0) cc_final: 0.8449 (t70) REVERT: AG 240 GLU cc_start: 0.9199 (tp30) cc_final: 0.8236 (tp30) REVERT: AG 244 MET cc_start: 0.9532 (ttp) cc_final: 0.9217 (ttt) REVERT: AI 24 ASP cc_start: 0.8821 (t0) cc_final: 0.8480 (t0) REVERT: AI 84 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8830 (mt-10) REVERT: AI 100 GLU cc_start: 0.8693 (tp30) cc_final: 0.8105 (tt0) REVERT: AI 125 GLU cc_start: 0.9127 (tp30) cc_final: 0.8744 (tp30) REVERT: AI 156 GLU cc_start: 0.8600 (mp0) cc_final: 0.8094 (mp0) REVERT: AI 240 GLU cc_start: 0.9130 (tp30) cc_final: 0.8779 (tp30) REVERT: AI 260 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8616 (tm-30) REVERT: AE 29 MET cc_start: 0.9200 (mtp) cc_final: 0.8508 (mtp) REVERT: AE 84 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8796 (tp30) REVERT: AE 94 ASP cc_start: 0.8295 (m-30) cc_final: 0.8057 (m-30) REVERT: AE 100 GLU cc_start: 0.9026 (tp30) cc_final: 0.8210 (tt0) REVERT: AE 156 GLU cc_start: 0.8675 (mp0) cc_final: 0.8059 (mp0) REVERT: AE 240 GLU cc_start: 0.9083 (tp30) cc_final: 0.8705 (tp30) REVERT: AE 244 MET cc_start: 0.9463 (ttp) cc_final: 0.9238 (ttt) REVERT: AE 260 GLN cc_start: 0.9243 (mt0) cc_final: 0.9028 (tm-30) REVERT: AN 30 GLU cc_start: 0.9267 (tt0) cc_final: 0.9025 (tt0) REVERT: AN 84 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8789 (mt-10) REVERT: AN 88 MET cc_start: 0.9060 (mtm) cc_final: 0.8104 (mmt) REVERT: AN 100 GLU cc_start: 0.8698 (tp30) cc_final: 0.8010 (tt0) REVERT: AN 125 GLU cc_start: 0.9155 (tp30) cc_final: 0.8695 (tp30) REVERT: AN 156 GLU cc_start: 0.8600 (mp0) cc_final: 0.8062 (mp0) REVERT: AN 240 GLU cc_start: 0.9083 (tp30) cc_final: 0.8874 (tp30) REVERT: AN 260 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8907 (tm-30) REVERT: AO 24 ASP cc_start: 0.8952 (t0) cc_final: 0.8626 (t0) REVERT: AO 30 GLU cc_start: 0.9119 (tt0) cc_final: 0.8857 (tm-30) REVERT: AO 125 GLU cc_start: 0.9166 (tp30) cc_final: 0.8737 (tp30) REVERT: AO 156 GLU cc_start: 0.8633 (mp0) cc_final: 0.7889 (mp0) REVERT: AO 260 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8901 (tm-30) REVERT: AP 30 GLU cc_start: 0.9230 (tt0) cc_final: 0.8870 (tt0) REVERT: AP 84 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8754 (mt-10) REVERT: AP 88 MET cc_start: 0.9232 (mtm) cc_final: 0.8249 (mmt) REVERT: AP 100 GLU cc_start: 0.8768 (tp30) cc_final: 0.8027 (tt0) REVERT: AP 156 GLU cc_start: 0.8629 (mp0) cc_final: 0.8111 (mp0) REVERT: AP 227 ASP cc_start: 0.9259 (t0) cc_final: 0.9034 (t0) REVERT: AP 240 GLU cc_start: 0.9099 (tp30) cc_final: 0.8760 (tp30) REVERT: AQ 84 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8851 (tp30) REVERT: AQ 100 GLU cc_start: 0.8934 (tp30) cc_final: 0.8088 (tt0) REVERT: AQ 125 GLU cc_start: 0.9158 (tp30) cc_final: 0.8868 (tp30) REVERT: AQ 156 GLU cc_start: 0.8513 (mp0) cc_final: 0.7902 (mp0) REVERT: AQ 240 GLU cc_start: 0.9232 (tp30) cc_final: 0.8769 (tp30) REVERT: AQ 260 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8581 (tm-30) REVERT: AR 30 GLU cc_start: 0.9196 (tt0) cc_final: 0.8937 (tt0) REVERT: AR 62 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8958 (mm-30) REVERT: AR 84 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8738 (mt-10) REVERT: AR 88 MET cc_start: 0.9376 (mtm) cc_final: 0.8408 (mmt) REVERT: AR 100 GLU cc_start: 0.8781 (tp30) cc_final: 0.8091 (tt0) REVERT: AR 125 GLU cc_start: 0.9255 (tp30) cc_final: 0.8792 (tp30) REVERT: AR 156 GLU cc_start: 0.8544 (mp0) cc_final: 0.8030 (mp0) REVERT: AR 227 ASP cc_start: 0.9308 (t0) cc_final: 0.9100 (t0) REVERT: AR 240 GLU cc_start: 0.9179 (tp30) cc_final: 0.8725 (tp30) REVERT: AR 244 MET cc_start: 0.9491 (ttp) cc_final: 0.9250 (ttt) REVERT: AH 29 MET cc_start: 0.9277 (mtp) cc_final: 0.9003 (mtp) REVERT: AH 30 GLU cc_start: 0.9156 (tt0) cc_final: 0.8896 (tm-30) REVERT: AH 84 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8838 (tp30) REVERT: AH 100 GLU cc_start: 0.8944 (tp30) cc_final: 0.8130 (tt0) REVERT: AH 125 GLU cc_start: 0.9107 (tp30) cc_final: 0.8821 (tp30) REVERT: AH 156 GLU cc_start: 0.8630 (mp0) cc_final: 0.7890 (mp0) REVERT: AH 240 GLU cc_start: 0.9182 (tp30) cc_final: 0.8805 (tp30) REVERT: AF 30 GLU cc_start: 0.9187 (tt0) cc_final: 0.8952 (tt0) REVERT: AF 84 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8888 (mt-10) REVERT: AF 88 MET cc_start: 0.9254 (mtp) cc_final: 0.8259 (mmt) REVERT: AF 100 GLU cc_start: 0.8787 (tp30) cc_final: 0.8110 (tt0) REVERT: AF 122 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7238 (mm-30) REVERT: AF 125 GLU cc_start: 0.9228 (tp30) cc_final: 0.8863 (tp30) REVERT: AF 156 GLU cc_start: 0.8677 (mp0) cc_final: 0.8154 (mp0) REVERT: AF 240 GLU cc_start: 0.9169 (tp30) cc_final: 0.8745 (tp30) REVERT: AF 260 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: AS 24 ASP cc_start: 0.9101 (t0) cc_final: 0.8733 (t0) REVERT: AS 29 MET cc_start: 0.9402 (mtm) cc_final: 0.8980 (mtp) REVERT: AS 125 GLU cc_start: 0.9303 (tp30) cc_final: 0.8913 (tp30) REVERT: AS 156 GLU cc_start: 0.8567 (mp0) cc_final: 0.7880 (mp0) REVERT: AS 240 GLU cc_start: 0.9228 (tp30) cc_final: 0.8695 (tp30) outliers start: 20 outliers final: 16 residues processed: 483 average time/residue: 0.2116 time to fit residues: 177.3644 Evaluate side-chains 486 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 468 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AJ residue 207 ILE Chi-restraints excluded: chain AJ residue 243 GLN Chi-restraints excluded: chain AJ residue 250 LEU Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AA residue 29 MET Chi-restraints excluded: chain AA residue 272 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AH residue 272 LEU Chi-restraints excluded: chain AF residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Chi-restraints excluded: chain AS residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 446 optimal weight: 5.9990 chunk 382 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 492 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 342 optimal weight: 6.9990 chunk 392 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 349 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AJ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 87 ASN AN 243 GLN ** AP 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.038699 restraints weight = 160902.623| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.34 r_work: 0.2572 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39560 Z= 0.183 Angle : 0.468 13.194 53300 Z= 0.251 Chirality : 0.033 0.143 6540 Planarity : 0.002 0.025 7100 Dihedral : 3.031 15.730 5600 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.49 % Allowed : 12.51 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.75 (0.12), residues: 5360 helix: 4.40 (0.07), residues: 3960 sheet: 1.23 (0.42), residues: 240 loop : -1.47 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAH 31 PHE 0.008 0.001 PHEAL 132 HIS 0.001 0.000 HISAR 213 Details of bonding type rmsd covalent geometry : bond 0.00388 (39560) covalent geometry : angle 0.46802 (53300) hydrogen bonds : bond 0.05201 ( 3420) hydrogen bonds : angle 2.93967 (10200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 464 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ao 29 MET cc_start: 0.9473 (mtt) cc_final: 0.8322 (mtt) REVERT: Ao 125 GLU cc_start: 0.9191 (tp30) cc_final: 0.8739 (tp30) REVERT: Ao 240 GLU cc_start: 0.9199 (tp30) cc_final: 0.8733 (tp30) REVERT: AJ 156 GLU cc_start: 0.8729 (mp0) cc_final: 0.7999 (mp0) REVERT: AJ 236 ASP cc_start: 0.9000 (t0) cc_final: 0.8393 (t0) REVERT: AJ 240 GLU cc_start: 0.9227 (tp30) cc_final: 0.8439 (tp30) REVERT: AJ 260 GLN cc_start: 0.9386 (tp-100) cc_final: 0.9180 (tp-100) REVERT: AK 24 ASP cc_start: 0.8935 (t0) cc_final: 0.8572 (t0) REVERT: AK 84 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9056 (tp30) REVERT: AK 100 GLU cc_start: 0.8917 (tp30) cc_final: 0.8196 (tt0) REVERT: AK 156 GLU cc_start: 0.8670 (mp0) cc_final: 0.7913 (mp0) REVERT: AK 240 GLU cc_start: 0.9214 (tp30) cc_final: 0.8551 (tp30) REVERT: AA 125 GLU cc_start: 0.9265 (tp30) cc_final: 0.8834 (tp30) REVERT: AA 156 GLU cc_start: 0.8647 (mp0) cc_final: 0.7623 (mp0) REVERT: AA 240 GLU cc_start: 0.9146 (tp30) cc_final: 0.8425 (tp30) REVERT: AA 260 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8828 (tm-30) REVERT: AL 24 ASP cc_start: 0.8968 (t0) cc_final: 0.8569 (t0) REVERT: AL 125 GLU cc_start: 0.9204 (tp30) cc_final: 0.8662 (tp30) REVERT: AL 156 GLU cc_start: 0.8593 (mp0) cc_final: 0.7543 (mp0) REVERT: AL 240 GLU cc_start: 0.9192 (tp30) cc_final: 0.8001 (tp30) REVERT: AL 260 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8822 (tm-30) REVERT: AB 24 ASP cc_start: 0.9101 (t0) cc_final: 0.8756 (t0) REVERT: AB 125 GLU cc_start: 0.9253 (tp30) cc_final: 0.8713 (tp30) REVERT: AB 156 GLU cc_start: 0.8771 (mp0) cc_final: 0.8113 (mp0) REVERT: AB 240 GLU cc_start: 0.9272 (tp30) cc_final: 0.8283 (tp30) REVERT: AC 30 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9030 (tm-30) REVERT: AC 84 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9023 (tp30) REVERT: AC 94 ASP cc_start: 0.8175 (m-30) cc_final: 0.7924 (m-30) REVERT: AC 156 GLU cc_start: 0.8765 (mp0) cc_final: 0.7998 (mp0) REVERT: AC 240 GLU cc_start: 0.9236 (tp30) cc_final: 0.8243 (tp30) REVERT: AC 260 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8727 (tm-30) REVERT: AD 156 GLU cc_start: 0.8648 (mp0) cc_final: 0.8176 (mp0) REVERT: AD 260 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8760 (tm-30) REVERT: AM 24 ASP cc_start: 0.8914 (t0) cc_final: 0.8517 (t0) REVERT: AM 29 MET cc_start: 0.9390 (mtt) cc_final: 0.9118 (mtt) REVERT: AM 84 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8933 (tp30) REVERT: AM 100 GLU cc_start: 0.8959 (tp30) cc_final: 0.8173 (tt0) REVERT: AM 156 GLU cc_start: 0.8627 (mp0) cc_final: 0.7991 (mp0) REVERT: AM 240 GLU cc_start: 0.9169 (tp30) cc_final: 0.8739 (tp30) REVERT: AM 260 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8862 (tm-30) REVERT: AG 125 GLU cc_start: 0.9192 (tp30) cc_final: 0.8850 (tp30) REVERT: AG 156 GLU cc_start: 0.8466 (mp0) cc_final: 0.7738 (mp0) REVERT: AG 227 ASP cc_start: 0.9333 (t0) cc_final: 0.9108 (t0) REVERT: AG 236 ASP cc_start: 0.8890 (t0) cc_final: 0.8473 (t70) REVERT: AG 240 GLU cc_start: 0.9233 (tp30) cc_final: 0.8343 (tp30) REVERT: AG 244 MET cc_start: 0.9526 (ttp) cc_final: 0.9259 (ttt) REVERT: AI 24 ASP cc_start: 0.8862 (t0) cc_final: 0.8514 (t0) REVERT: AI 84 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8873 (mt-10) REVERT: AI 88 MET cc_start: 0.9373 (mtp) cc_final: 0.8376 (mmt) REVERT: AI 100 GLU cc_start: 0.8673 (tp30) cc_final: 0.8092 (tt0) REVERT: AI 125 GLU cc_start: 0.9138 (tp30) cc_final: 0.8772 (tp30) REVERT: AI 156 GLU cc_start: 0.8608 (mp0) cc_final: 0.7889 (mp0) REVERT: AI 240 GLU cc_start: 0.9147 (tp30) cc_final: 0.8785 (tp30) REVERT: AI 260 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8633 (tm-30) REVERT: AE 29 MET cc_start: 0.9235 (mtp) cc_final: 0.8613 (mtp) REVERT: AE 84 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8772 (tp30) REVERT: AE 100 GLU cc_start: 0.9035 (tp30) cc_final: 0.8241 (tt0) REVERT: AE 156 GLU cc_start: 0.8687 (mp0) cc_final: 0.8049 (mp0) REVERT: AE 240 GLU cc_start: 0.9096 (tp30) cc_final: 0.8727 (tp30) REVERT: AE 244 MET cc_start: 0.9477 (ttp) cc_final: 0.9245 (ttt) REVERT: AE 260 GLN cc_start: 0.9266 (mt0) cc_final: 0.9026 (tm-30) REVERT: AN 30 GLU cc_start: 0.9288 (tt0) cc_final: 0.9045 (tt0) REVERT: AN 62 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9116 (tm-30) REVERT: AN 84 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8791 (mt-10) REVERT: AN 88 MET cc_start: 0.9058 (mtm) cc_final: 0.8072 (mmt) REVERT: AN 100 GLU cc_start: 0.8682 (tp30) cc_final: 0.7995 (tt0) REVERT: AN 125 GLU cc_start: 0.9162 (tp30) cc_final: 0.8708 (tp30) REVERT: AN 156 GLU cc_start: 0.8570 (mp0) cc_final: 0.7988 (mp0) REVERT: AN 240 GLU cc_start: 0.9107 (tp30) cc_final: 0.8769 (tp30) REVERT: AN 260 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8825 (tm-30) REVERT: AO 24 ASP cc_start: 0.8981 (t0) cc_final: 0.8654 (t0) REVERT: AO 30 GLU cc_start: 0.9089 (tt0) cc_final: 0.8796 (tm-30) REVERT: AO 125 GLU cc_start: 0.9186 (tp30) cc_final: 0.8750 (tp30) REVERT: AO 156 GLU cc_start: 0.8622 (mp0) cc_final: 0.7856 (mp0) REVERT: AO 260 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8904 (tm-30) REVERT: AP 30 GLU cc_start: 0.9248 (tt0) cc_final: 0.8894 (tt0) REVERT: AP 84 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8742 (mt-10) REVERT: AP 88 MET cc_start: 0.9335 (mtm) cc_final: 0.8271 (mmt) REVERT: AP 100 GLU cc_start: 0.8760 (tp30) cc_final: 0.8024 (tt0) REVERT: AP 156 GLU cc_start: 0.8636 (mp0) cc_final: 0.8101 (mp0) REVERT: AP 227 ASP cc_start: 0.9277 (t0) cc_final: 0.9031 (t0) REVERT: AP 240 GLU cc_start: 0.9126 (tp30) cc_final: 0.8795 (tp30) REVERT: AQ 84 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8843 (tp30) REVERT: AQ 100 GLU cc_start: 0.8912 (tp30) cc_final: 0.8081 (tt0) REVERT: AQ 125 GLU cc_start: 0.9183 (tp30) cc_final: 0.8881 (tp30) REVERT: AQ 156 GLU cc_start: 0.8494 (mp0) cc_final: 0.7911 (mp0) REVERT: AQ 240 GLU cc_start: 0.9245 (tp30) cc_final: 0.8755 (tp30) REVERT: AQ 260 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8720 (tm-30) REVERT: AR 30 GLU cc_start: 0.9193 (tt0) cc_final: 0.8940 (tt0) REVERT: AR 84 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8766 (mt-10) REVERT: AR 88 MET cc_start: 0.9374 (mtm) cc_final: 0.8418 (mmt) REVERT: AR 100 GLU cc_start: 0.8764 (tp30) cc_final: 0.8086 (tt0) REVERT: AR 125 GLU cc_start: 0.9289 (tp30) cc_final: 0.8820 (tp30) REVERT: AR 156 GLU cc_start: 0.8559 (mp0) cc_final: 0.7998 (mp0) REVERT: AR 227 ASP cc_start: 0.9336 (t0) cc_final: 0.9082 (t0) REVERT: AR 240 GLU cc_start: 0.9201 (tp30) cc_final: 0.8745 (tp30) REVERT: AR 244 MET cc_start: 0.9494 (ttp) cc_final: 0.9249 (ttt) REVERT: AH 84 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8838 (tp30) REVERT: AH 100 GLU cc_start: 0.8946 (tp30) cc_final: 0.8129 (tt0) REVERT: AH 125 GLU cc_start: 0.9197 (tp30) cc_final: 0.8877 (tp30) REVERT: AH 156 GLU cc_start: 0.8646 (mp0) cc_final: 0.7894 (mp0) REVERT: AH 240 GLU cc_start: 0.9225 (tp30) cc_final: 0.8700 (tp30) REVERT: AF 30 GLU cc_start: 0.9186 (tt0) cc_final: 0.8954 (tt0) REVERT: AF 84 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8903 (mt-10) REVERT: AF 88 MET cc_start: 0.9280 (mtp) cc_final: 0.8263 (mmt) REVERT: AF 100 GLU cc_start: 0.8783 (tp30) cc_final: 0.8118 (tt0) REVERT: AF 125 GLU cc_start: 0.9223 (tp30) cc_final: 0.8858 (tp30) REVERT: AF 156 GLU cc_start: 0.8658 (mp0) cc_final: 0.8123 (mp0) REVERT: AF 240 GLU cc_start: 0.9190 (tp30) cc_final: 0.8788 (tp30) REVERT: AF 260 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: AS 24 ASP cc_start: 0.9124 (t0) cc_final: 0.8756 (t0) REVERT: AS 29 MET cc_start: 0.9426 (mtm) cc_final: 0.9187 (mtp) REVERT: AS 125 GLU cc_start: 0.9343 (tp30) cc_final: 0.8974 (tp30) REVERT: AS 156 GLU cc_start: 0.8560 (mp0) cc_final: 0.7846 (mp0) REVERT: AS 240 GLU cc_start: 0.9243 (tp30) cc_final: 0.8731 (tp30) outliers start: 21 outliers final: 16 residues processed: 476 average time/residue: 0.2043 time to fit residues: 169.0533 Evaluate side-chains 476 residues out of total 4260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 458 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ao residue 250 LEU Chi-restraints excluded: chain AJ residue 207 ILE Chi-restraints excluded: chain AJ residue 243 GLN Chi-restraints excluded: chain AJ residue 250 LEU Chi-restraints excluded: chain AK residue 250 LEU Chi-restraints excluded: chain AA residue 29 MET Chi-restraints excluded: chain AA residue 272 LEU Chi-restraints excluded: chain AL residue 207 ILE Chi-restraints excluded: chain AB residue 108 ASP Chi-restraints excluded: chain AB residue 207 ILE Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AM residue 250 LEU Chi-restraints excluded: chain AE residue 250 LEU Chi-restraints excluded: chain AH residue 272 LEU Chi-restraints excluded: chain AF residue 260 GLN Chi-restraints excluded: chain AS residue 108 ASP Chi-restraints excluded: chain AS residue 207 ILE Chi-restraints excluded: chain AS residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 323 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 394 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 491 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 462 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AJ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 260 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 = 0.2956 r_free = 0.2956 target = 0.046335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.039625 restraints weight = 159861.082| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.39 r_work: 0.2604 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39560 Z= 0.133 Angle : 0.437 13.003 53300 Z= 0.234 Chirality : 0.032 0.160 6540 Planarity : 0.002 0.026 7100 Dihedral : 2.975 15.672 5600 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.45 % Allowed : 12.68 % Favored : 86.88 % 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: 4.82 (0.12), residues: 5360 helix: 4.45 (0.07), residues: 3960 sheet: 1.30 (0.42), residues: 240 loop : -1.48 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAA 210 PHE 0.007 0.001 PHEAL 132 HIS 0.001 0.000 HISAE 213 Details of bonding type rmsd covalent geometry : bond 0.00271 (39560) covalent geometry : angle 0.43714 (53300) hydrogen bonds : bond 0.04916 ( 3420) hydrogen bonds : angle 2.81176 (10200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7334.22 seconds wall clock time: 127 minutes 49.91 seconds (7669.91 seconds total)