Starting phenix.real_space_refine on Sun Sep 13 17:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tu7_10590/09_2026/6tu7_10590.map" } resolution = 3.1 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= 0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Br 4 7.06 5 P 10 5.49 5 Mg 4 5.21 5 S 126 5.16 5 C 15262 2.51 5 N 4040 2.21 5 O 4618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24064 Number of models: 1 Model: "" Number of chains: 3 Chain: "AP1" Number of atoms: 6060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6060 Classifications: {'peptide': 766} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 739} Chain: "BP1" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "BP1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: GP1, CP1, DP1, EP1 Time building chain proxies: 8.47, per 1000 atoms: 0.35 Number of scatterers: 24064 At special positions: 0 Unit cell: (137.34, 223.45, 170.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 4 34.99 S 126 16.00 P 10 15.00 Mg 4 11.99 O 4618 8.00 N 4040 7.00 C 15262 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 38 sheets defined 47.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'AP1' and resid 4 through 15 removed outlier: 3.804A pdb=" N ILEAP1 8 " --> pdb=" O THRAP1 4 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALAP1 15 " --> pdb=" O ALAAP1 11 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 109 through 123 removed outlier: 3.765A pdb=" N LYSAP1 123 " --> pdb=" O HISAP1 119 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 147 through 157 removed outlier: 3.565A pdb=" N ILEAP1 151 " --> pdb=" O THRAP1 147 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THRAP1 157 " --> pdb=" O ARGAP1 153 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 166 through 181 removed outlier: 3.848A pdb=" N CYSAP1 170 " --> pdb=" O HISAP1 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VALAP1 181 " --> pdb=" O ASNAP1 177 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 197 through 210 Processing helix chain 'AP1' and resid 218 through 226 Processing helix chain 'AP1' and resid 227 through 235 Processing helix chain 'AP1' and resid 274 through 278 Processing helix chain 'AP1' and resid 287 through 297 removed outlier: 4.323A pdb=" N TYRAP1 291 " --> pdb=" O TYRAP1 287 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 298 through 305 Processing helix chain 'AP1' and resid 309 through 313 removed outlier: 3.898A pdb=" N TYRAP1 313 " --> pdb=" O VALAP1 310 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 329 through 342 removed outlier: 3.690A pdb=" N GLUAP1 333 " --> pdb=" O VALAP1 329 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N METAP1 342 " --> pdb=" O SERAP1 338 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 345 through 363 Processing helix chain 'AP1' and resid 385 through 395 removed outlier: 3.543A pdb=" N ASNAP1 390 " --> pdb=" O METAP1 386 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 399 through 408 Processing helix chain 'AP1' and resid 424 through 453 Processing helix chain 'AP1' and resid 454 through 456 No H-bonds generated for 'chain 'AP1' and resid 454 through 456' Processing helix chain 'AP1' and resid 480 through 512 Processing helix chain 'AP1' and resid 524 through 533 Processing helix chain 'AP1' and resid 537 through 548 Processing helix chain 'AP1' and resid 552 through 564 Processing helix chain 'AP1' and resid 565 through 567 No H-bonds generated for 'chain 'AP1' and resid 565 through 567' Processing helix chain 'AP1' and resid 596 through 602 removed outlier: 3.643A pdb=" N LYSAP1 600 " --> pdb=" O SERAP1 596 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 606 through 615 Processing helix chain 'AP1' and resid 618 through 625 removed outlier: 4.065A pdb=" N PHEAP1 625 " --> pdb=" O VALAP1 621 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 640 through 659 removed outlier: 3.821A pdb=" N THRAP1 659 " --> pdb=" O LEUAP1 655 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 679 through 690 removed outlier: 3.676A pdb=" N GLNAP1 686 " --> pdb=" O LYSAP1 682 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 691 through 700 Processing helix chain 'AP1' and resid 708 through 716 Processing helix chain 'AP1' and resid 730 through 743 Processing helix chain 'AP1' and resid 745 through 747 No H-bonds generated for 'chain 'AP1' and resid 745 through 747' Processing helix chain 'AP1' and resid 759 through 767 Processing helix chain 'BP1' and resid 57 through 62 removed outlier: 3.578A pdb=" N THRBP1 61 " --> pdb=" O ASPBP1 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSBP1 62 " --> pdb=" O GLUBP1 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP1' and resid 57 through 62' Processing helix chain 'BP1' and resid 79 through 93 Processing helix chain 'BP1' and resid 98 through 102 removed outlier: 3.609A pdb=" N GLUBP1 101 " --> pdb=" O ALABP1 98 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 113 through 127 removed outlier: 4.392A pdb=" N ARGBP1 117 " --> pdb=" O PROBP1 113 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 138 through 145 removed outlier: 3.716A pdb=" N LEUBP1 143 " --> pdb=" O ALABP1 139 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 173 through 176 removed outlier: 3.811A pdb=" N ILEBP1 176 " --> pdb=" O PROBP1 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP1' and resid 173 through 176' Processing helix chain 'BP1' and resid 182 through 194 Processing helix chain 'BP1' and resid 195 through 198 Processing helix chain 'BP1' and resid 206 through 218 Processing helix chain 'BP1' and resid 223 through 231 Processing helix chain 'BP1' and resid 253 through 258 removed outlier: 3.703A pdb=" N CYSBP1 258 " --> pdb=" O GLUBP1 254 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 259 through 263 Processing helix chain 'BP1' and resid 264 through 269 Processing helix chain 'BP1' and resid 274 through 284 removed outlier: 3.551A pdb=" N PHEBP1 280 " --> pdb=" O HISBP1 276 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 290 through 295 removed outlier: 3.633A pdb=" N LEUBP1 294 " --> pdb=" O ILEBP1 290 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 309 through 320 removed outlier: 3.613A pdb=" N ARGBP1 313 " --> pdb=" O GLYBP1 309 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THRBP1 320 " --> pdb=" O ARGBP1 316 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 338 through 349 Processing helix chain 'BP1' and resid 352 through 356 removed outlier: 3.964A pdb=" N GLNBP1 355 " --> pdb=" O THRBP1 352 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 360 through 367 Processing helix chain 'BP1' and resid 370 through 375 Processing helix chain 'CP1' and resid 57 through 62 removed outlier: 3.578A pdb=" N THRCP1 61 " --> pdb=" O ASPCP1 57 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSCP1 62 " --> pdb=" O GLUCP1 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP1' and resid 57 through 62' Processing helix chain 'CP1' and resid 79 through 93 Processing helix chain 'CP1' and resid 98 through 102 removed outlier: 3.609A pdb=" N GLUCP1 101 " --> pdb=" O ALACP1 98 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 113 through 127 removed outlier: 4.393A pdb=" N ARGCP1 117 " --> pdb=" O PROCP1 113 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 138 through 145 removed outlier: 3.715A pdb=" N LEUCP1 143 " --> pdb=" O ALACP1 139 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 173 through 176 removed outlier: 3.811A pdb=" N ILECP1 176 " --> pdb=" O PROCP1 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP1' and resid 173 through 176' Processing helix chain 'CP1' and resid 182 through 194 Processing helix chain 'CP1' and resid 195 through 198 Processing helix chain 'CP1' and resid 206 through 218 Processing helix chain 'CP1' and resid 223 through 231 Processing helix chain 'CP1' and resid 253 through 258 removed outlier: 3.703A pdb=" N CYSCP1 258 " --> pdb=" O GLUCP1 254 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 259 through 263 Processing helix chain 'CP1' and resid 264 through 269 Processing helix chain 'CP1' and resid 274 through 284 removed outlier: 3.552A pdb=" N PHECP1 280 " --> pdb=" O HISCP1 276 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 290 through 295 removed outlier: 3.631A pdb=" N LEUCP1 294 " --> pdb=" O ILECP1 290 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 309 through 320 removed outlier: 3.612A pdb=" N ARGCP1 313 " --> pdb=" O GLYCP1 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THRCP1 320 " --> pdb=" O ARGCP1 316 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 338 through 349 Processing helix chain 'CP1' and resid 352 through 356 removed outlier: 3.964A pdb=" N GLNCP1 355 " --> pdb=" O THRCP1 352 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 360 through 367 Processing helix chain 'CP1' and resid 370 through 375 Processing helix chain 'DP1' and resid 57 through 62 removed outlier: 3.578A pdb=" N THRDP1 61 " --> pdb=" O ASPDP1 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSDP1 62 " --> pdb=" O GLUDP1 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'DP1' and resid 57 through 62' Processing helix chain 'DP1' and resid 79 through 93 Processing helix chain 'DP1' and resid 98 through 102 removed outlier: 3.609A pdb=" N GLUDP1 101 " --> pdb=" O ALADP1 98 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 113 through 127 removed outlier: 4.393A pdb=" N ARGDP1 117 " --> pdb=" O PRODP1 113 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 138 through 145 removed outlier: 3.715A pdb=" N LEUDP1 143 " --> pdb=" O ALADP1 139 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 173 through 176 removed outlier: 3.811A pdb=" N ILEDP1 176 " --> pdb=" O PRODP1 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'DP1' and resid 173 through 176' Processing helix chain 'DP1' and resid 182 through 194 Processing helix chain 'DP1' and resid 195 through 198 Processing helix chain 'DP1' and resid 206 through 218 Processing helix chain 'DP1' and resid 223 through 231 Processing helix chain 'DP1' and resid 253 through 258 removed outlier: 3.703A pdb=" N CYSDP1 258 " --> pdb=" O GLUDP1 254 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 259 through 263 Processing helix chain 'DP1' and resid 264 through 269 Processing helix chain 'DP1' and resid 274 through 284 removed outlier: 3.552A pdb=" N PHEDP1 280 " --> pdb=" O HISDP1 276 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 290 through 295 removed outlier: 3.631A pdb=" N LEUDP1 294 " --> pdb=" O ILEDP1 290 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 309 through 320 removed outlier: 3.612A pdb=" N ARGDP1 313 " --> pdb=" O GLYDP1 309 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THRDP1 320 " --> pdb=" O ARGDP1 316 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 338 through 349 Processing helix chain 'DP1' and resid 352 through 356 removed outlier: 3.964A pdb=" N GLNDP1 355 " --> pdb=" O THRDP1 352 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 360 through 367 Processing helix chain 'DP1' and resid 370 through 375 Processing helix chain 'EP1' and resid 57 through 62 removed outlier: 3.578A pdb=" N THREP1 61 " --> pdb=" O ASPEP1 57 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSEP1 62 " --> pdb=" O GLUEP1 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'EP1' and resid 57 through 62' Processing helix chain 'EP1' and resid 79 through 93 Processing helix chain 'EP1' and resid 98 through 102 removed outlier: 3.609A pdb=" N GLUEP1 101 " --> pdb=" O ALAEP1 98 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 113 through 127 removed outlier: 4.393A pdb=" N ARGEP1 117 " --> pdb=" O PROEP1 113 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 138 through 145 removed outlier: 3.715A pdb=" N LEUEP1 143 " --> pdb=" O ALAEP1 139 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 173 through 176 removed outlier: 3.811A pdb=" N ILEEP1 176 " --> pdb=" O PROEP1 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'EP1' and resid 173 through 176' Processing helix chain 'EP1' and resid 182 through 194 Processing helix chain 'EP1' and resid 195 through 198 Processing helix chain 'EP1' and resid 206 through 218 Processing helix chain 'EP1' and resid 223 through 231 Processing helix chain 'EP1' and resid 253 through 258 removed outlier: 3.703A pdb=" N CYSEP1 258 " --> pdb=" O GLUEP1 254 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 259 through 263 Processing helix chain 'EP1' and resid 264 through 269 Processing helix chain 'EP1' and resid 274 through 284 removed outlier: 3.552A pdb=" N PHEEP1 280 " --> pdb=" O HISEP1 276 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 290 through 295 removed outlier: 3.632A pdb=" N LEUEP1 294 " --> pdb=" O ILEEP1 290 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 309 through 320 removed outlier: 3.613A pdb=" N ARGEP1 313 " --> pdb=" O GLYEP1 309 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THREP1 320 " --> pdb=" O ARGEP1 316 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 338 through 349 Processing helix chain 'EP1' and resid 352 through 356 removed outlier: 3.964A pdb=" N GLNEP1 355 " --> pdb=" O THREP1 352 " (cutoff:3.500A) Processing helix chain 'EP1' and resid 360 through 367 Processing helix chain 'EP1' and resid 370 through 375 Processing helix chain 'GP1' and resid 4 through 15 removed outlier: 3.805A pdb=" N ILEGP1 8 " --> pdb=" O THRGP1 4 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VALGP1 15 " --> pdb=" O ALAGP1 11 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 109 through 123 removed outlier: 3.765A pdb=" N LYSGP1 123 " --> pdb=" O HISGP1 119 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 147 through 157 removed outlier: 3.566A pdb=" N ILEGP1 151 " --> pdb=" O THRGP1 147 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THRGP1 157 " --> pdb=" O ARGGP1 153 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 166 through 181 removed outlier: 3.848A pdb=" N CYSGP1 170 " --> pdb=" O HISGP1 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VALGP1 181 " --> pdb=" O ASNGP1 177 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 197 through 210 Processing helix chain 'GP1' and resid 218 through 226 Processing helix chain 'GP1' and resid 227 through 235 Processing helix chain 'GP1' and resid 274 through 278 Processing helix chain 'GP1' and resid 287 through 297 removed outlier: 4.322A pdb=" N TYRGP1 291 " --> pdb=" O TYRGP1 287 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 298 through 305 Processing helix chain 'GP1' and resid 309 through 313 removed outlier: 3.899A pdb=" N TYRGP1 313 " --> pdb=" O VALGP1 310 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 329 through 342 removed outlier: 3.690A pdb=" N GLUGP1 333 " --> pdb=" O VALGP1 329 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N METGP1 342 " --> pdb=" O SERGP1 338 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 345 through 363 Processing helix chain 'GP1' and resid 385 through 395 removed outlier: 3.542A pdb=" N ASNGP1 390 " --> pdb=" O METGP1 386 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 399 through 408 Processing helix chain 'GP1' and resid 424 through 453 Processing helix chain 'GP1' and resid 454 through 456 No H-bonds generated for 'chain 'GP1' and resid 454 through 456' Processing helix chain 'GP1' and resid 480 through 512 Processing helix chain 'GP1' and resid 524 through 533 Processing helix chain 'GP1' and resid 537 through 548 Processing helix chain 'GP1' and resid 552 through 564 Processing helix chain 'GP1' and resid 565 through 567 No H-bonds generated for 'chain 'GP1' and resid 565 through 567' Processing helix chain 'GP1' and resid 596 through 602 removed outlier: 3.643A pdb=" N LYSGP1 600 " --> pdb=" O SERGP1 596 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 606 through 615 Processing helix chain 'GP1' and resid 618 through 625 removed outlier: 4.065A pdb=" N PHEGP1 625 " --> pdb=" O VALGP1 621 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 640 through 659 removed outlier: 3.820A pdb=" N THRGP1 659 " --> pdb=" O LEUGP1 655 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 679 through 690 removed outlier: 3.677A pdb=" N GLNGP1 686 " --> pdb=" O LYSGP1 682 " (cutoff:3.500A) Processing helix chain 'GP1' and resid 691 through 700 Processing helix chain 'GP1' and resid 708 through 716 Processing helix chain 'GP1' and resid 730 through 743 Processing helix chain 'GP1' and resid 745 through 747 No H-bonds generated for 'chain 'GP1' and resid 745 through 747' Processing helix chain 'GP1' and resid 759 through 767 Processing sheet with id=AA1, first strand: chain 'AP1' and resid 80 through 82 removed outlier: 6.809A pdb=" N LYSAP1 54 " --> pdb=" O ILEAP1 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AP1' and resid 128 through 130 removed outlier: 3.699A pdb=" N ILEAP1 134 " --> pdb=" O PHEAP1 663 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYSAP1 666 " --> pdb=" O SERAP1 190 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLNAP1 185 " --> pdb=" O GLYAP1 466 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEUAP1 468 " --> pdb=" O GLNAP1 185 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILEAP1 187 " --> pdb=" O LEUAP1 468 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILEAP1 470 " --> pdb=" O ILEAP1 187 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VALAP1 189 " --> pdb=" O ILEAP1 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AP1' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'AP1' and resid 367 through 370 Processing sheet with id=AA5, first strand: chain 'AP1' and resid 409 through 413 removed outlier: 3.669A pdb=" N LYSAP1 410 " --> pdb=" O GLYAP1 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AP1' and resid 570 through 572 Processing sheet with id=AA7, first strand: chain 'AP1' and resid 705 through 707 Processing sheet with id=AA8, first strand: chain 'BP1' and resid 30 through 33 removed outlier: 6.798A pdb=" N LEUBP1 9 " --> pdb=" O LEUBP1 105 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THRBP1 107 " --> pdb=" O LEUBP1 9 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VALBP1 11 " --> pdb=" O THRBP1 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'BP1' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'BP1' and resid 72 through 73 Processing sheet with id=AB2, first strand: chain 'BP1' and resid 170 through 171 Processing sheet with id=AB3, first strand: chain 'BP1' and resid 170 through 171 removed outlier: 3.615A pdb=" N SERBP1 156 " --> pdb=" O SERBP1 301 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILEBP1 298 " --> pdb=" O VALBP1 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'BP1' and resid 239 through 242 Processing sheet with id=AB5, first strand: chain 'CP1' and resid 30 through 33 removed outlier: 6.798A pdb=" N LEUCP1 9 " --> pdb=" O LEUCP1 105 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THRCP1 107 " --> pdb=" O LEUCP1 9 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VALCP1 11 " --> pdb=" O THRCP1 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'CP1' and resid 54 through 55 Processing sheet with id=AB7, first strand: chain 'CP1' and resid 72 through 73 Processing sheet with id=AB8, first strand: chain 'CP1' and resid 170 through 171 Processing sheet with id=AB9, first strand: chain 'CP1' and resid 170 through 171 removed outlier: 3.616A pdb=" N SERCP1 156 " --> pdb=" O SERCP1 301 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILECP1 298 " --> pdb=" O VALCP1 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'CP1' and resid 239 through 242 Processing sheet with id=AC2, first strand: chain 'DP1' and resid 30 through 33 removed outlier: 6.798A pdb=" N LEUDP1 9 " --> pdb=" O LEUDP1 105 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THRDP1 107 " --> pdb=" O LEUDP1 9 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VALDP1 11 " --> pdb=" O THRDP1 107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'DP1' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'DP1' and resid 72 through 73 Processing sheet with id=AC5, first strand: chain 'DP1' and resid 170 through 171 Processing sheet with id=AC6, first strand: chain 'DP1' and resid 170 through 171 removed outlier: 3.617A pdb=" N SERDP1 156 " --> pdb=" O SERDP1 301 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILEDP1 298 " --> pdb=" O VALDP1 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'DP1' and resid 239 through 242 Processing sheet with id=AC8, first strand: chain 'EP1' and resid 30 through 33 removed outlier: 6.798A pdb=" N LEUEP1 9 " --> pdb=" O LEUEP1 105 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THREP1 107 " --> pdb=" O LEUEP1 9 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VALEP1 11 " --> pdb=" O THREP1 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'EP1' and resid 54 through 55 Processing sheet with id=AD1, first strand: chain 'EP1' and resid 72 through 73 Processing sheet with id=AD2, first strand: chain 'EP1' and resid 170 through 171 Processing sheet with id=AD3, first strand: chain 'EP1' and resid 170 through 171 removed outlier: 3.616A pdb=" N SEREP1 156 " --> pdb=" O SEREP1 301 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILEEP1 298 " --> pdb=" O VALEP1 331 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'EP1' and resid 239 through 242 Processing sheet with id=AD5, first strand: chain 'GP1' and resid 80 through 82 removed outlier: 6.810A pdb=" N LYSGP1 54 " --> pdb=" O ILEGP1 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'GP1' and resid 128 through 130 removed outlier: 3.698A pdb=" N ILEGP1 134 " --> pdb=" O PHEGP1 663 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYSGP1 666 " --> pdb=" O SERGP1 190 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLNGP1 185 " --> pdb=" O GLYGP1 466 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEUGP1 468 " --> pdb=" O GLNGP1 185 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILEGP1 187 " --> pdb=" O LEUGP1 468 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILEGP1 470 " --> pdb=" O ILEGP1 187 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VALGP1 189 " --> pdb=" O ILEGP1 470 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'GP1' and resid 236 through 237 Processing sheet with id=AD8, first strand: chain 'GP1' and resid 367 through 370 Processing sheet with id=AD9, first strand: chain 'GP1' and resid 409 through 413 removed outlier: 3.668A pdb=" N LYSGP1 410 " --> pdb=" O GLYGP1 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'GP1' and resid 570 through 572 Processing sheet with id=AE2, first strand: chain 'GP1' and resid 705 through 707 1104 hydrogen bonds defined for protein. 2994 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: 7.57 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7860 1.35 - 1.49: 6084 1.49 - 1.62: 10384 1.62 - 1.76: 0 1.76 - 1.90: 214 Bond restraints: 24542 Sorted by residual: bond pdb=" C9 9UEBP1 403 " pdb=" N1 9UEBP1 403 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C9 9UECP1 403 " pdb=" N1 9UECP1 403 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C9 9UEDP1 403 " pdb=" N1 9UEDP1 403 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" C9 9UEEP1 403 " pdb=" N1 9UEEP1 403 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C11 9UECP1 403 " pdb=" N2 9UECP1 403 " ideal model delta sigma weight residual 1.351 1.396 -0.045 2.00e-02 2.50e+03 5.13e+00 ... (remaining 24537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 32701 2.03 - 4.05: 401 4.05 - 6.08: 80 6.08 - 8.10: 12 8.10 - 10.13: 12 Bond angle restraints: 33206 Sorted by residual: angle pdb=" N ILEGP1 721 " pdb=" CA ILEGP1 721 " pdb=" C ILEGP1 721 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N ILEAP1 721 " pdb=" CA ILEAP1 721 " pdb=" C ILEAP1 721 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C20 9UEDP1 403 " pdb=" C8 9UEDP1 403 " pdb=" C7 9UEDP1 403 " ideal model delta sigma weight residual 118.25 108.12 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C20 9UECP1 403 " pdb=" C8 9UECP1 403 " pdb=" C7 9UECP1 403 " ideal model delta sigma weight residual 118.25 108.13 10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C20 9UEEP1 403 " pdb=" C8 9UEEP1 403 " pdb=" C7 9UEEP1 403 " ideal model delta sigma weight residual 118.25 108.13 10.12 3.00e+00 1.11e-01 1.14e+01 ... (remaining 33201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 14564 35.21 - 70.42: 226 70.42 - 105.63: 60 105.63 - 140.84: 56 140.84 - 176.05: 32 Dihedral angle restraints: 14938 sinusoidal: 6220 harmonic: 8718 Sorted by residual: dihedral pdb=" O1B ADPBP1 401 " pdb=" O3A ADPBP1 401 " pdb=" PB ADPBP1 401 " pdb=" PA ADPBP1 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.79 126.21 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" O1B ADPDP1 401 " pdb=" O3A ADPDP1 401 " pdb=" PB ADPDP1 401 " pdb=" PA ADPDP1 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.82 126.18 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" O1B ADPEP1 401 " pdb=" O3A ADPEP1 401 " pdb=" PB ADPEP1 401 " pdb=" PA ADPEP1 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.83 126.17 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 14935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3639 0.119 - 0.237: 57 0.237 - 0.356: 0 0.356 - 0.474: 12 0.474 - 0.593: 4 Chirality restraints: 3712 Sorted by residual: chirality pdb=" C6 9UEDP1 403 " pdb=" N 9UEDP1 403 " pdb=" C29 9UEDP1 403 " pdb=" C5 9UEDP1 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.57 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" C6 9UEEP1 403 " pdb=" N 9UEEP1 403 " pdb=" C29 9UEEP1 403 " pdb=" C5 9UEEP1 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.57 0.59 2.00e-01 2.50e+01 8.72e+00 chirality pdb=" C6 9UECP1 403 " pdb=" N 9UECP1 403 " pdb=" C29 9UECP1 403 " pdb=" C5 9UECP1 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.56 0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 3709 not shown) Planarity restraints: 4252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALDP1 164 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRODP1 165 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRODP1 165 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRODP1 165 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALCP1 164 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PROCP1 165 " 0.061 5.00e-02 4.00e+02 pdb=" CA PROCP1 165 " -0.018 5.00e-02 4.00e+02 pdb=" CD PROCP1 165 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALBP1 164 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PROBP1 165 " -0.061 5.00e-02 4.00e+02 pdb=" CA PROBP1 165 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROBP1 165 " 0.019 5.00e-02 4.00e+02 ... (remaining 4249 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 753 2.70 - 3.25: 23339 3.25 - 3.80: 35415 3.80 - 4.35: 47435 4.35 - 4.90: 82554 Nonbonded interactions: 189496 Sorted by model distance: nonbonded pdb=" O GLYEP1 157 " pdb=" OG1 THREP1 304 " model vdw 2.154 3.040 nonbonded pdb=" O GLYCP1 157 " pdb=" OG1 THRCP1 304 " model vdw 2.155 3.040 nonbonded pdb=" O GLYBP1 157 " pdb=" OG1 THRBP1 304 " model vdw 2.156 3.040 nonbonded pdb=" O GLYDP1 157 " pdb=" OG1 THRDP1 304 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THRAP1 186 " pdb=" OG1 THRAP1 659 " model vdw 2.249 3.040 ... (remaining 189491 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: 0.07 Found NCS groups: ncs_group { reference = chain 'AP1' selection = chain 'GP1' } ncs_group { reference = chain 'BP1' selection = chain 'CP1' selection = chain 'DP1' selection = chain 'EP1' } 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: 11.820 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.110 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.006 0.047 24542 Z= 0.266 Angle : 0.655 10.131 33206 Z= 0.335 Chirality : 0.056 0.593 3712 Planarity : 0.004 0.035 4252 Dihedral : 19.346 176.049 9334 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.05 % Allowed : 5.13 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % 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: -2.48 (0.13), residues: 3002 helix: -1.14 (0.13), residues: 1202 sheet: -0.92 (0.22), residues: 500 loop : -2.37 (0.14), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAP1 606 TYR 0.010 0.001 TYRDP1 70 PHE 0.013 0.001 PHEAP1 116 TRP 0.012 0.002 TRPBP1 341 HIS 0.004 0.001 HISCP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 (24542) covalent geometry : angle 0.65472 / 0.34 (33206) hydrogen bonds : bond 0.17882 / 11.69 ( 1096) hydrogen bonds : angle 6.60990 / 4.62 ( 2994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.950 Fit side-chains REVERT: AP1 18 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.6952 (p) REVERT: AP1 31 PHE cc_start: 0.6954 (m-80) cc_final: 0.6723 (m-80) REVERT: AP1 45 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: AP1 218 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5462 (tt) REVERT: AP1 653 MET cc_start: 0.8271 (mmm) cc_final: 0.8066 (mmp) REVERT: AP1 674 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8124 (mtmt) REVERT: BP1 48 MET cc_start: 0.8890 (ptt) cc_final: 0.8556 (ptt) REVERT: BP1 49 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7980 (mt-10) REVERT: CP1 29 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7893 (ttp-170) REVERT: CP1 96 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7653 (tpm170) REVERT: CP1 122 GLN cc_start: 0.8693 (tt0) cc_final: 0.8420 (tt0) REVERT: DP1 48 MET cc_start: 0.8663 (ptt) cc_final: 0.8104 (ptm) REVERT: DP1 83 MET cc_start: 0.8843 (tpt) cc_final: 0.8492 (tpt) REVERT: DP1 96 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7636 (tpm170) REVERT: DP1 122 GLN cc_start: 0.8680 (tt0) cc_final: 0.8424 (tt0) REVERT: DP1 158 ASP cc_start: 0.8634 (t0) cc_final: 0.8413 (t0) REVERT: DP1 306 MET cc_start: 0.8691 (mtp) cc_final: 0.8321 (mmt) REVERT: DP1 326 MET cc_start: 0.8946 (mmp) cc_final: 0.8720 (mmp) REVERT: EP1 122 GLN cc_start: 0.8603 (tt0) cc_final: 0.8335 (tt0) REVERT: EP1 326 MET cc_start: 0.8993 (mmp) cc_final: 0.8760 (mmp) REVERT: GP1 18 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6398 (p) REVERT: GP1 218 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5489 (tt) outliers start: 54 outliers final: 24 residues processed: 255 average time/residue: 0.1746 time to fit residues: 69.8594 Evaluate side-chains 177 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 45 GLU Chi-restraints excluded: chain AP1 residue 218 LEU Chi-restraints excluded: chain AP1 residue 471 PHE Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain BP1 residue 35 ILE Chi-restraints excluded: chain BP1 residue 149 THR Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 325 THR Chi-restraints excluded: chain BP1 residue 371 VAL Chi-restraints excluded: chain CP1 residue 25 ASP Chi-restraints excluded: chain CP1 residue 145 SER Chi-restraints excluded: chain CP1 residue 149 THR Chi-restraints excluded: chain CP1 residue 268 LEU Chi-restraints excluded: chain CP1 residue 325 THR Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 35 ILE Chi-restraints excluded: chain DP1 residue 145 SER Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 371 VAL Chi-restraints excluded: chain EP1 residue 35 ILE Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 325 THR Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 471 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085443 restraints weight = 32915.923| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.97 r_work: 0.2693 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24542 Z= 0.105 Angle : 0.535 7.135 33206 Z= 0.270 Chirality : 0.043 0.135 3712 Planarity : 0.004 0.039 4252 Dihedral : 23.915 179.242 3522 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.41 % Allowed : 7.48 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3002 helix: 0.34 (0.15), residues: 1198 sheet: -0.08 (0.23), residues: 500 loop : -1.61 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGEP1 373 TYR 0.011 0.001 TYRAP1 716 PHE 0.020 0.001 PHEGP1 353 TRP 0.008 0.001 TRPCP1 80 HIS 0.003 0.001 HISAP1 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (24542) covalent geometry : angle 0.53487 / 0.27 (33206) hydrogen bonds : bond 0.04287 / 2.81 ( 1096) hydrogen bonds : angle 4.71138 / 3.29 ( 2994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.965 Fit side-chains REVERT: AP1 31 PHE cc_start: 0.7099 (m-80) cc_final: 0.6633 (m-80) REVERT: AP1 45 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: AP1 353 PHE cc_start: 0.7651 (m-10) cc_final: 0.7108 (m-80) REVERT: AP1 377 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7931 (p0) REVERT: AP1 611 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7482 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8083 (mtmt) REVERT: BP1 49 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8296 (mt-10) REVERT: BP1 238 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: CP1 96 ARG cc_start: 0.8951 (mtm180) cc_final: 0.7531 (tpm170) REVERT: DP1 48 MET cc_start: 0.8368 (ptt) cc_final: 0.7740 (ptm) REVERT: DP1 83 MET cc_start: 0.9143 (tpt) cc_final: 0.8890 (tpt) REVERT: DP1 96 ARG cc_start: 0.8937 (mtm180) cc_final: 0.7433 (tpm170) REVERT: DP1 306 MET cc_start: 0.9139 (mtp) cc_final: 0.8845 (mmt) REVERT: DP1 326 MET cc_start: 0.9222 (mmp) cc_final: 0.8953 (mmp) REVERT: EP1 49 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8311 (mt-10) REVERT: EP1 83 MET cc_start: 0.9261 (tpt) cc_final: 0.8773 (tpt) REVERT: EP1 122 GLN cc_start: 0.9068 (tt0) cc_final: 0.8838 (tt0) REVERT: EP1 238 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: EP1 326 MET cc_start: 0.9296 (mmp) cc_final: 0.9082 (mmp) REVERT: GP1 129 THR cc_start: 0.7795 (m) cc_final: 0.7579 (t) REVERT: GP1 150 TRP cc_start: 0.8443 (m100) cc_final: 0.8017 (m100) REVERT: GP1 218 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4902 (tp) REVERT: GP1 232 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7136 (mm-30) REVERT: GP1 353 PHE cc_start: 0.7453 (m-10) cc_final: 0.7004 (m-80) REVERT: GP1 377 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7852 (p0) REVERT: GP1 396 MET cc_start: 0.8880 (mtt) cc_final: 0.8576 (mtm) REVERT: GP1 439 MET cc_start: 0.8540 (mmt) cc_final: 0.8166 (tpt) REVERT: GP1 611 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7448 (mm-30) REVERT: GP1 653 MET cc_start: 0.8300 (mmp) cc_final: 0.8028 (mmm) outliers start: 37 outliers final: 11 residues processed: 198 average time/residue: 0.1727 time to fit residues: 54.8420 Evaluate side-chains 168 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 45 GLU Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 377 ASP Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain BP1 residue 238 GLU Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 191 MET Chi-restraints excluded: chain CP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 152 optimal weight: 0.0050 chunk 211 optimal weight: 0.0670 chunk 139 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 280 optimal weight: 0.1980 chunk 182 optimal weight: 0.0270 chunk 256 optimal weight: 10.0000 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088110 restraints weight = 33036.283| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.93 r_work: 0.2750 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24542 Z= 0.083 Angle : 0.484 8.144 33206 Z= 0.239 Chirality : 0.043 0.211 3712 Planarity : 0.003 0.032 4252 Dihedral : 23.621 178.095 3493 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.37 % Allowed : 8.32 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3002 helix: 1.01 (0.16), residues: 1208 sheet: 0.43 (0.23), residues: 496 loop : -1.21 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGEP1 373 TYR 0.006 0.001 TYRCP1 144 PHE 0.014 0.001 PHEGP1 712 TRP 0.006 0.001 TRPCP1 80 HIS 0.003 0.001 HISDP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 (24542) covalent geometry : angle 0.48436 / 0.24 (33206) hydrogen bonds : bond 0.03318 / 2.18 ( 1096) hydrogen bonds : angle 4.29240 / 3.00 ( 2994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.009 Fit side-chains REVERT: AP1 353 PHE cc_start: 0.7468 (m-10) cc_final: 0.6895 (m-80) REVERT: AP1 611 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7532 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8144 (mtmt) REVERT: BP1 48 MET cc_start: 0.8580 (ptt) cc_final: 0.8087 (ptt) REVERT: BP1 49 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8121 (mt-10) REVERT: BP1 138 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: CP1 96 ARG cc_start: 0.8910 (mtm180) cc_final: 0.7557 (tpm170) REVERT: DP1 49 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8504 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8918 (mtm180) cc_final: 0.7478 (tpm170) REVERT: DP1 306 MET cc_start: 0.9092 (mtp) cc_final: 0.8795 (mmt) REVERT: DP1 326 MET cc_start: 0.9235 (mmp) cc_final: 0.8932 (mmp) REVERT: EP1 83 MET cc_start: 0.9237 (tpt) cc_final: 0.8733 (tpt) REVERT: EP1 238 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: EP1 326 MET cc_start: 0.9321 (mmp) cc_final: 0.9108 (mmp) REVERT: GP1 129 THR cc_start: 0.7737 (m) cc_final: 0.7434 (t) REVERT: GP1 218 LEU cc_start: 0.5334 (OUTLIER) cc_final: 0.5038 (tp) REVERT: GP1 225 MET cc_start: 0.8120 (mmt) cc_final: 0.7905 (mmm) REVERT: GP1 353 PHE cc_start: 0.7222 (m-10) cc_final: 0.6888 (m-80) REVERT: GP1 611 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7406 (mm-30) outliers start: 36 outliers final: 15 residues processed: 211 average time/residue: 0.1725 time to fit residues: 58.6158 Evaluate side-chains 179 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain BP1 residue 44 ILE Chi-restraints excluded: chain BP1 residue 138 GLN Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain CP1 residue 191 MET Chi-restraints excluded: chain CP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 252 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082904 restraints weight = 33341.568| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.99 r_work: 0.2638 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 24542 Z= 0.309 Angle : 0.630 8.259 33206 Z= 0.315 Chirality : 0.051 0.267 3712 Planarity : 0.005 0.061 4252 Dihedral : 23.569 179.105 3490 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.75 % Allowed : 9.46 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3002 helix: 0.94 (0.15), residues: 1182 sheet: 0.37 (0.23), residues: 496 loop : -1.22 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGBP1 178 TYR 0.014 0.002 TYRGP1 207 PHE 0.019 0.002 PHEGP1 116 TRP 0.014 0.002 TRPEP1 341 HIS 0.005 0.001 HISBP1 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.31 (24542) covalent geometry : angle 0.62978 / 0.32 (33206) hydrogen bonds : bond 0.05319 / 3.52 ( 1096) hydrogen bonds : angle 4.44402 / 3.11 ( 2994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.982 Fit side-chains REVERT: AP1 31 PHE cc_start: 0.6912 (m-80) cc_final: 0.6382 (m-80) REVERT: AP1 353 PHE cc_start: 0.7814 (m-10) cc_final: 0.7478 (m-80) REVERT: AP1 611 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7601 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8147 (mtmt) REVERT: BP1 49 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8369 (mt-10) REVERT: CP1 96 ARG cc_start: 0.8984 (mtm180) cc_final: 0.7599 (tpm170) REVERT: DP1 96 ARG cc_start: 0.8980 (mtm180) cc_final: 0.7572 (tpm170) REVERT: DP1 306 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9047 (mmt) REVERT: DP1 326 MET cc_start: 0.9248 (mmp) cc_final: 0.8946 (mmp) REVERT: EP1 238 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: GP1 129 THR cc_start: 0.7701 (m) cc_final: 0.7477 (t) REVERT: GP1 218 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5242 (tp) REVERT: GP1 353 PHE cc_start: 0.7579 (m-10) cc_final: 0.7174 (m-80) REVERT: GP1 377 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7807 (p0) REVERT: GP1 611 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7533 (mm-30) outliers start: 46 outliers final: 33 residues processed: 184 average time/residue: 0.1626 time to fit residues: 49.3361 Evaluate side-chains 184 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 471 PHE Chi-restraints excluded: chain AP1 residue 624 LEU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain BP1 residue 371 VAL Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 191 MET Chi-restraints excluded: chain CP1 residue 235 SER Chi-restraints excluded: chain CP1 residue 306 MET Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 306 MET Chi-restraints excluded: chain DP1 residue 371 VAL Chi-restraints excluded: chain EP1 residue 44 ILE Chi-restraints excluded: chain EP1 residue 48 MET Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 297 ASN Chi-restraints excluded: chain EP1 residue 325 THR Chi-restraints excluded: chain EP1 residue 371 VAL Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 215 ASN Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 471 PHE Chi-restraints excluded: chain GP1 residue 608 ASP Chi-restraints excluded: chain GP1 residue 624 LEU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 62 optimal weight: 0.0470 chunk 165 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085612 restraints weight = 32762.940| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.92 r_work: 0.2702 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24542 Z= 0.111 Angle : 0.509 9.422 33206 Z= 0.251 Chirality : 0.044 0.159 3712 Planarity : 0.003 0.031 4252 Dihedral : 23.135 173.537 3488 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.67 % Allowed : 10.11 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3002 helix: 1.30 (0.15), residues: 1190 sheet: 0.57 (0.24), residues: 496 loop : -0.98 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBP1 373 TYR 0.006 0.001 TYRAP1 541 PHE 0.008 0.001 PHEGP1 581 TRP 0.008 0.001 TRPBP1 80 HIS 0.004 0.001 HISCP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (24542) covalent geometry : angle 0.50906 / 0.25 (33206) hydrogen bonds : bond 0.03695 / 2.44 ( 1096) hydrogen bonds : angle 4.21933 / 2.95 ( 2994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.834 Fit side-chains REVERT: AP1 216 MET cc_start: 0.2929 (tpp) cc_final: 0.2122 (tmm) REVERT: AP1 353 PHE cc_start: 0.7660 (m-10) cc_final: 0.7330 (m-80) REVERT: AP1 377 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7864 (p0) REVERT: AP1 441 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7529 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8071 (mtmt) REVERT: BP1 49 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8192 (mt-10) REVERT: CP1 96 ARG cc_start: 0.8953 (mtm180) cc_final: 0.7622 (tpm170) REVERT: CP1 326 MET cc_start: 0.9216 (mmp) cc_final: 0.8896 (mmp) REVERT: DP1 49 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8399 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8944 (mtm180) cc_final: 0.7577 (tpm170) REVERT: DP1 306 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8831 (mmt) REVERT: DP1 326 MET cc_start: 0.9244 (mmp) cc_final: 0.8935 (mmp) REVERT: EP1 238 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: GP1 129 THR cc_start: 0.7675 (m) cc_final: 0.7398 (t) REVERT: GP1 218 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5384 (tp) REVERT: GP1 353 PHE cc_start: 0.7477 (m-10) cc_final: 0.7059 (m-80) REVERT: GP1 377 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (p0) REVERT: GP1 441 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: GP1 611 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7453 (mm-30) REVERT: GP1 653 MET cc_start: 0.8312 (mmp) cc_final: 0.8099 (mmp) outliers start: 44 outliers final: 28 residues processed: 191 average time/residue: 0.1622 time to fit residues: 50.4130 Evaluate side-chains 191 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 377 ASP Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 191 MET Chi-restraints excluded: chain CP1 residue 235 SER Chi-restraints excluded: chain CP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 306 MET Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 297 ASN Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 382 MET Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086519 restraints weight = 33000.280| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.91 r_work: 0.2716 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24542 Z= 0.102 Angle : 0.495 11.517 33206 Z= 0.242 Chirality : 0.044 0.194 3712 Planarity : 0.003 0.034 4252 Dihedral : 22.634 171.101 3488 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 10.11 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 3002 helix: 1.56 (0.15), residues: 1192 sheet: 0.66 (0.24), residues: 502 loop : -0.79 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGEP1 96 TYR 0.007 0.001 TYRDP1 144 PHE 0.010 0.001 PHEGP1 116 TRP 0.009 0.001 TRPCP1 80 HIS 0.004 0.001 HISCP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (24542) covalent geometry : angle 0.49504 / 0.24 (33206) hydrogen bonds : bond 0.03457 / 2.29 ( 1096) hydrogen bonds : angle 4.10706 / 2.87 ( 2994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.971 Fit side-chains REVERT: AP1 353 PHE cc_start: 0.7445 (m-10) cc_final: 0.7098 (m-80) REVERT: AP1 441 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7567 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (mtmt) REVERT: BP1 49 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8225 (mt-10) REVERT: BP1 138 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: CP1 96 ARG cc_start: 0.8951 (mtm180) cc_final: 0.7622 (tpm170) REVERT: CP1 326 MET cc_start: 0.9207 (mmp) cc_final: 0.8900 (mmp) REVERT: DP1 49 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8443 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8935 (mtm180) cc_final: 0.7601 (tpm170) REVERT: DP1 306 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8834 (mmt) REVERT: DP1 326 MET cc_start: 0.9230 (mmp) cc_final: 0.8887 (mmp) REVERT: EP1 238 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: GP1 129 THR cc_start: 0.7682 (m) cc_final: 0.7450 (t) REVERT: GP1 218 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5488 (tp) REVERT: GP1 353 PHE cc_start: 0.7366 (m-10) cc_final: 0.7052 (m-80) REVERT: GP1 441 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: GP1 611 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7425 (mm-30) outliers start: 45 outliers final: 28 residues processed: 200 average time/residue: 0.1640 time to fit residues: 53.8516 Evaluate side-chains 194 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 45 GLU Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 138 GLN Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 235 SER Chi-restraints excluded: chain CP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 48 MET Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 306 MET Chi-restraints excluded: chain DP1 residue 325 THR Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 297 ASN Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 21 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 285 optimal weight: 0.8980 chunk 166 optimal weight: 0.0970 chunk 288 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 205 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087874 restraints weight = 33358.675| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.01 r_work: 0.2747 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24542 Z= 0.078 Angle : 0.478 10.310 33206 Z= 0.230 Chirality : 0.042 0.184 3712 Planarity : 0.003 0.032 4252 Dihedral : 22.108 170.774 3488 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.37 % Allowed : 10.87 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 3002 helix: 1.88 (0.16), residues: 1184 sheet: 0.84 (0.24), residues: 494 loop : -0.59 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGEP1 96 TYR 0.007 0.001 TYRDP1 144 PHE 0.008 0.001 PHEGP1 497 TRP 0.008 0.001 TRPBP1 80 HIS 0.004 0.001 HISBP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.08 (24542) covalent geometry : angle 0.47817 / 0.23 (33206) hydrogen bonds : bond 0.02880 / 1.91 ( 1096) hydrogen bonds : angle 3.99338 / 2.79 ( 2994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.974 Fit side-chains REVERT: AP1 21 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7546 (t) REVERT: AP1 353 PHE cc_start: 0.7272 (m-10) cc_final: 0.6962 (m-80) REVERT: AP1 441 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7517 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8111 (mtmt) REVERT: BP1 49 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8159 (mt-10) REVERT: BP1 138 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8433 (mt0) REVERT: CP1 96 ARG cc_start: 0.8928 (mtm180) cc_final: 0.7634 (tpm170) REVERT: CP1 326 MET cc_start: 0.9189 (mmp) cc_final: 0.8920 (mmp) REVERT: DP1 49 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8486 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8904 (mtm180) cc_final: 0.7556 (tpm170) REVERT: DP1 306 MET cc_start: 0.9062 (mtp) cc_final: 0.8782 (mmt) REVERT: DP1 326 MET cc_start: 0.9230 (mmp) cc_final: 0.8867 (mmp) REVERT: EP1 238 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: GP1 218 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5173 (tp) REVERT: GP1 353 PHE cc_start: 0.7186 (m-10) cc_final: 0.6874 (m-80) REVERT: GP1 377 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7733 (p0) REVERT: GP1 441 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: GP1 611 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7428 (mm-30) outliers start: 36 outliers final: 24 residues processed: 198 average time/residue: 0.1678 time to fit residues: 53.6406 Evaluate side-chains 196 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 21 VAL Chi-restraints excluded: chain AP1 residue 45 GLU Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 48 MET Chi-restraints excluded: chain BP1 residue 138 GLN Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 235 SER Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain EP1 residue 48 MET Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 126 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.084186 restraints weight = 33034.847| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.94 r_work: 0.2673 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24542 Z= 0.220 Angle : 0.573 9.343 33206 Z= 0.282 Chirality : 0.048 0.265 3712 Planarity : 0.004 0.047 4252 Dihedral : 22.361 171.259 3487 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.71 % Allowed : 10.49 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3002 helix: 1.65 (0.15), residues: 1182 sheet: 0.64 (0.23), residues: 522 loop : -0.74 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGCP1 291 TYR 0.017 0.001 TYRAP1 714 PHE 0.015 0.001 PHEGP1 116 TRP 0.013 0.002 TRPCP1 341 HIS 0.005 0.001 HISBP1 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.22 (24542) covalent geometry : angle 0.57254 / 0.28 (33206) hydrogen bonds : bond 0.04460 / 2.96 ( 1096) hydrogen bonds : angle 4.16578 / 2.92 ( 2994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.002 Fit side-chains REVERT: AP1 353 PHE cc_start: 0.7493 (m-10) cc_final: 0.7178 (m-80) REVERT: AP1 441 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7485 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8123 (mtmt) REVERT: AP1 715 GLN cc_start: 0.7541 (tt0) cc_final: 0.7315 (tt0) REVERT: BP1 49 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8297 (mt-10) REVERT: CP1 96 ARG cc_start: 0.8960 (mtm180) cc_final: 0.7613 (tpm170) REVERT: CP1 326 MET cc_start: 0.9217 (mmp) cc_final: 0.8908 (mmp) REVERT: DP1 49 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8476 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8930 (mtm180) cc_final: 0.7570 (tpm170) REVERT: DP1 306 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8915 (mmt) REVERT: EP1 238 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: GP1 218 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5312 (tp) REVERT: GP1 353 PHE cc_start: 0.7399 (m-10) cc_final: 0.7072 (m-80) REVERT: GP1 377 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7658 (p0) REVERT: GP1 441 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: GP1 653 MET cc_start: 0.8304 (mmp) cc_final: 0.8030 (mmp) outliers start: 45 outliers final: 32 residues processed: 193 average time/residue: 0.1659 time to fit residues: 52.3386 Evaluate side-chains 194 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 35 ILE Chi-restraints excluded: chain BP1 residue 46 VAL Chi-restraints excluded: chain BP1 residue 48 MET Chi-restraints excluded: chain BP1 residue 149 THR Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain BP1 residue 325 THR Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 325 THR Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 35 ILE Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 306 MET Chi-restraints excluded: chain DP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 371 VAL Chi-restraints excluded: chain EP1 residue 48 MET Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 268 LEU Chi-restraints excluded: chain GP1 residue 3 VAL Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 32 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.085917 restraints weight = 33140.779| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.95 r_work: 0.2701 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24542 Z= 0.118 Angle : 0.520 12.441 33206 Z= 0.253 Chirality : 0.045 0.203 3712 Planarity : 0.003 0.032 4252 Dihedral : 22.188 171.179 3486 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.52 % Allowed : 10.68 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 3002 helix: 1.74 (0.15), residues: 1190 sheet: 0.73 (0.24), residues: 502 loop : -0.64 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGEP1 373 TYR 0.018 0.001 TYRAP1 714 PHE 0.009 0.001 PHEGP1 581 TRP 0.009 0.001 TRPBP1 80 HIS 0.004 0.001 HISCP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (24542) covalent geometry : angle 0.52017 / 0.25 (33206) hydrogen bonds : bond 0.03637 / 2.41 ( 1096) hydrogen bonds : angle 4.09075 / 2.86 ( 2994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.960 Fit side-chains REVERT: AP1 216 MET cc_start: 0.2644 (tpp) cc_final: 0.1792 (tmm) REVERT: AP1 353 PHE cc_start: 0.7436 (m-10) cc_final: 0.7150 (m-80) REVERT: AP1 441 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7517 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8128 (mtmt) REVERT: AP1 715 GLN cc_start: 0.7515 (tt0) cc_final: 0.7282 (tt0) REVERT: BP1 49 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8233 (mt-10) REVERT: CP1 96 ARG cc_start: 0.8957 (mtm180) cc_final: 0.7634 (tpm170) REVERT: CP1 326 MET cc_start: 0.9203 (mmp) cc_final: 0.8910 (mmp) REVERT: DP1 49 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8494 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8931 (mtm180) cc_final: 0.7632 (tpm170) REVERT: DP1 306 MET cc_start: 0.9111 (mtp) cc_final: 0.8843 (mmt) REVERT: EP1 238 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: GP1 218 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5455 (tp) REVERT: GP1 353 PHE cc_start: 0.7378 (m-10) cc_final: 0.7068 (m-80) REVERT: GP1 377 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7748 (p0) REVERT: GP1 441 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7391 (tm-30) outliers start: 40 outliers final: 33 residues processed: 196 average time/residue: 0.1644 time to fit residues: 52.6657 Evaluate side-chains 199 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 45 GLU Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 35 ILE Chi-restraints excluded: chain BP1 residue 48 MET Chi-restraints excluded: chain BP1 residue 149 THR Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain BP1 residue 325 THR Chi-restraints excluded: chain BP1 residue 371 VAL Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 44 ILE Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 371 VAL Chi-restraints excluded: chain EP1 residue 48 MET Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 297 ASN Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 2 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 289 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.083703 restraints weight = 33062.384| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.92 r_work: 0.2668 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24542 Z= 0.233 Angle : 0.589 11.832 33206 Z= 0.290 Chirality : 0.049 0.282 3712 Planarity : 0.004 0.051 4252 Dihedral : 22.374 171.539 3484 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.82 % Allowed : 10.56 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3002 helix: 1.55 (0.15), residues: 1182 sheet: 0.61 (0.23), residues: 522 loop : -0.75 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGBP1 373 TYR 0.017 0.001 TYRAP1 714 PHE 0.016 0.002 PHEGP1 556 TRP 0.013 0.002 TRPEP1 341 HIS 0.004 0.001 HISCP1 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.23 (24542) covalent geometry : angle 0.58886 / 0.29 (33206) hydrogen bonds : bond 0.04627 / 3.07 ( 1096) hydrogen bonds : angle 4.23009 / 2.96 ( 2994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.973 Fit side-chains REVERT: AP1 216 MET cc_start: 0.2768 (tpp) cc_final: 0.1879 (tmm) REVERT: AP1 353 PHE cc_start: 0.7708 (m-10) cc_final: 0.7419 (m-80) REVERT: AP1 441 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: AP1 611 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7446 (mm-30) REVERT: AP1 674 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8115 (mtmt) REVERT: AP1 715 GLN cc_start: 0.7517 (tt0) cc_final: 0.7283 (tt0) REVERT: BP1 49 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8296 (mt-10) REVERT: CP1 96 ARG cc_start: 0.9006 (mtm180) cc_final: 0.7716 (tpm170) REVERT: CP1 326 MET cc_start: 0.9212 (mmp) cc_final: 0.8898 (mmp) REVERT: DP1 49 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8494 (mt-10) REVERT: DP1 96 ARG cc_start: 0.8917 (mtm180) cc_final: 0.7621 (tpm170) REVERT: DP1 306 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8938 (mmt) REVERT: EP1 238 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: GP1 218 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5453 (tp) REVERT: GP1 353 PHE cc_start: 0.7550 (m-10) cc_final: 0.7175 (m-80) REVERT: GP1 377 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7700 (p0) REVERT: GP1 441 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7412 (tm-30) outliers start: 48 outliers final: 36 residues processed: 193 average time/residue: 0.1615 time to fit residues: 51.8037 Evaluate side-chains 197 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 18 VAL Chi-restraints excluded: chain AP1 residue 57 VAL Chi-restraints excluded: chain AP1 residue 66 LEU Chi-restraints excluded: chain AP1 residue 239 THR Chi-restraints excluded: chain AP1 residue 441 GLU Chi-restraints excluded: chain AP1 residue 674 LYS Chi-restraints excluded: chain AP1 residue 767 THR Chi-restraints excluded: chain AP1 residue 768 LYS Chi-restraints excluded: chain BP1 residue 35 ILE Chi-restraints excluded: chain BP1 residue 46 VAL Chi-restraints excluded: chain BP1 residue 48 MET Chi-restraints excluded: chain BP1 residue 149 THR Chi-restraints excluded: chain BP1 residue 268 LEU Chi-restraints excluded: chain BP1 residue 306 MET Chi-restraints excluded: chain BP1 residue 325 THR Chi-restraints excluded: chain BP1 residue 371 VAL Chi-restraints excluded: chain CP1 residue 35 ILE Chi-restraints excluded: chain CP1 residue 48 MET Chi-restraints excluded: chain CP1 residue 235 SER Chi-restraints excluded: chain CP1 residue 325 THR Chi-restraints excluded: chain CP1 residue 371 VAL Chi-restraints excluded: chain DP1 residue 35 ILE Chi-restraints excluded: chain DP1 residue 149 THR Chi-restraints excluded: chain DP1 residue 268 LEU Chi-restraints excluded: chain DP1 residue 306 MET Chi-restraints excluded: chain DP1 residue 325 THR Chi-restraints excluded: chain DP1 residue 371 VAL Chi-restraints excluded: chain EP1 residue 48 MET Chi-restraints excluded: chain EP1 residue 149 THR Chi-restraints excluded: chain EP1 residue 235 SER Chi-restraints excluded: chain EP1 residue 238 GLU Chi-restraints excluded: chain EP1 residue 297 ASN Chi-restraints excluded: chain GP1 residue 3 VAL Chi-restraints excluded: chain GP1 residue 18 VAL Chi-restraints excluded: chain GP1 residue 57 VAL Chi-restraints excluded: chain GP1 residue 94 VAL Chi-restraints excluded: chain GP1 residue 128 THR Chi-restraints excluded: chain GP1 residue 143 LEU Chi-restraints excluded: chain GP1 residue 218 LEU Chi-restraints excluded: chain GP1 residue 377 ASP Chi-restraints excluded: chain GP1 residue 441 GLU Chi-restraints excluded: chain GP1 residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 141 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 94 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086526 restraints weight = 33056.749| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.91 r_work: 0.2720 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24542 Z= 0.096 Angle : 0.513 11.826 33206 Z= 0.249 Chirality : 0.044 0.188 3712 Planarity : 0.003 0.035 4252 Dihedral : 22.140 171.433 3484 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.44 % Allowed : 11.09 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 3002 helix: 1.86 (0.15), residues: 1178 sheet: 0.74 (0.24), residues: 502 loop : -0.55 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGBP1 373 TYR 0.018 0.001 TYRAP1 714 PHE 0.014 0.001 PHEAP1 712 TRP 0.009 0.001 TRPBP1 80 HIS 0.004 0.001 HISBP1 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (24542) covalent geometry : angle 0.51282 / 0.25 (33206) hydrogen bonds : bond 0.03439 / 2.28 ( 1096) hydrogen bonds : angle 4.08345 / 2.86 ( 2994) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7559.43 seconds wall clock time: 129 minutes 14.93 seconds (7754.93 seconds total)