Starting phenix.real_space_refine on Wed Aug 27 02:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1r_9318/08_2025/6n1r_9318_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 252 5.16 5 C 28896 2.51 5 N 8292 2.21 5 O 8604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46044 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.30, per 1000 atoms: 0.09 Number of scatterers: 46044 At special positions: 0 Unit cell: (186.16, 189.28, 159.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 252 16.00 O 8604 8.00 N 8292 7.00 C 28896 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 60 sheets defined 54.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 30 Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 386 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 386 Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL B 390 " --> pdb=" O HIS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 30 Processing helix chain 'C' and resid 40 through 53 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.669A pdb=" N VAL C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 386 Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL C 390 " --> pdb=" O HIS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 30 Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'D' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 386 Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 30 Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 223 through 234 removed outlier: 3.733A pdb=" N ILE E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 280 Processing helix chain 'E' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 386 Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL E 390 " --> pdb=" O HIS E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 412 Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS E 436 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 477 removed outlier: 3.704A pdb=" N VAL E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 64 through 75 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 128 through 133 Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 Processing helix chain 'F' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 386 Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL F 390 " --> pdb=" O HIS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 Processing helix chain 'F' and resid 414 through 423 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS F 436 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 30 Processing helix chain 'G' and resid 40 through 53 Processing helix chain 'G' and resid 64 through 75 Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL G 166 " --> pdb=" O PRO G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'G' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 280 Processing helix chain 'G' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE G 313 " --> pdb=" O SER G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 386 Processing helix chain 'G' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL G 390 " --> pdb=" O HIS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 412 Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 477 removed outlier: 3.706A pdb=" N VAL G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 30 Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 64 through 75 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL H 166 " --> pdb=" O PRO H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 198 Processing helix chain 'H' and resid 202 through 208 Processing helix chain 'H' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 280 Processing helix chain 'H' and resid 309 through 321 removed outlier: 3.731A pdb=" N ILE H 313 " --> pdb=" O SER H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 386 Processing helix chain 'H' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL H 390 " --> pdb=" O HIS H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 412 Processing helix chain 'H' and resid 414 through 423 Processing helix chain 'H' and resid 425 through 429 Processing helix chain 'H' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS H 436 " --> pdb=" O LEU H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 30 Processing helix chain 'I' and resid 40 through 53 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'I' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL I 166 " --> pdb=" O PRO I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 198 Processing helix chain 'I' and resid 202 through 208 Processing helix chain 'I' and resid 223 through 234 removed outlier: 3.733A pdb=" N ILE I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 280 Processing helix chain 'I' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE I 313 " --> pdb=" O SER I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 386 Processing helix chain 'I' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL I 390 " --> pdb=" O HIS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 412 Processing helix chain 'I' and resid 414 through 423 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 477 removed outlier: 3.706A pdb=" N VAL I 461 " --> pdb=" O LYS I 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 30 Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'J' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL J 166 " --> pdb=" O PRO J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 198 Processing helix chain 'J' and resid 202 through 208 Processing helix chain 'J' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE J 227 " --> pdb=" O GLY J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 280 Processing helix chain 'J' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE J 313 " --> pdb=" O SER J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 386 Processing helix chain 'J' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL J 390 " --> pdb=" O HIS J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 412 Processing helix chain 'J' and resid 414 through 423 Processing helix chain 'J' and resid 425 through 429 Processing helix chain 'J' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS J 436 " --> pdb=" O LEU J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL J 461 " --> pdb=" O LYS J 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 30 Processing helix chain 'K' and resid 40 through 53 Processing helix chain 'K' and resid 64 through 75 Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'K' and resid 162 through 168 removed outlier: 3.669A pdb=" N VAL K 166 " --> pdb=" O PRO K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 198 Processing helix chain 'K' and resid 202 through 208 Processing helix chain 'K' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE K 227 " --> pdb=" O GLY K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 280 Processing helix chain 'K' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE K 313 " --> pdb=" O SER K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 386 Processing helix chain 'K' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL K 390 " --> pdb=" O HIS K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 412 Processing helix chain 'K' and resid 414 through 423 Processing helix chain 'K' and resid 425 through 429 Processing helix chain 'K' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS K 436 " --> pdb=" O LEU K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL K 461 " --> pdb=" O LYS K 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 30 Processing helix chain 'L' and resid 40 through 53 Processing helix chain 'L' and resid 64 through 75 Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'L' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL L 166 " --> pdb=" O PRO L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 198 Processing helix chain 'L' and resid 202 through 208 Processing helix chain 'L' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE L 227 " --> pdb=" O GLY L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 280 Processing helix chain 'L' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE L 313 " --> pdb=" O SER L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 386 Processing helix chain 'L' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL L 390 " --> pdb=" O HIS L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 412 Processing helix chain 'L' and resid 414 through 423 Processing helix chain 'L' and resid 425 through 429 Processing helix chain 'L' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS L 436 " --> pdb=" O LEU L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL L 461 " --> pdb=" O LYS L 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 330 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG A 243 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 288 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 63 Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 330 Processing sheet with id=AA9, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG B 243 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 288 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 330 Processing sheet with id=AB5, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.429A pdb=" N ARG C 243 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 288 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'D' and resid 62 through 63 Processing sheet with id=AB8, first strand: chain 'D' and resid 143 through 145 Processing sheet with id=AB9, first strand: chain 'D' and resid 324 through 330 Processing sheet with id=AC1, first strand: chain 'D' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG D 243 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 288 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 335 Processing sheet with id=AC3, first strand: chain 'E' and resid 62 through 63 Processing sheet with id=AC4, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AC5, first strand: chain 'E' and resid 324 through 330 Processing sheet with id=AC6, first strand: chain 'E' and resid 243 through 247 removed outlier: 6.429A pdb=" N ARG E 243 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 288 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 63 Processing sheet with id=AC9, first strand: chain 'F' and resid 143 through 145 Processing sheet with id=AD1, first strand: chain 'F' and resid 324 through 330 Processing sheet with id=AD2, first strand: chain 'F' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG F 243 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA F 288 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 332 through 335 Processing sheet with id=AD4, first strand: chain 'G' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain 'G' and resid 143 through 145 Processing sheet with id=AD6, first strand: chain 'G' and resid 324 through 330 Processing sheet with id=AD7, first strand: chain 'G' and resid 243 through 247 removed outlier: 6.427A pdb=" N ARG G 243 " --> pdb=" O THR G 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA G 288 " --> pdb=" O GLU G 303 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 332 through 335 Processing sheet with id=AD9, first strand: chain 'H' and resid 62 through 63 Processing sheet with id=AE1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AE2, first strand: chain 'H' and resid 324 through 330 Processing sheet with id=AE3, first strand: chain 'H' and resid 243 through 247 removed outlier: 6.427A pdb=" N ARG H 243 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA H 288 " --> pdb=" O GLU H 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 332 through 335 Processing sheet with id=AE5, first strand: chain 'I' and resid 62 through 63 Processing sheet with id=AE6, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AE7, first strand: chain 'I' and resid 324 through 330 Processing sheet with id=AE8, first strand: chain 'I' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG I 243 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA I 288 " --> pdb=" O GLU I 303 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 332 through 335 Processing sheet with id=AF1, first strand: chain 'J' and resid 62 through 63 Processing sheet with id=AF2, first strand: chain 'J' and resid 143 through 145 Processing sheet with id=AF3, first strand: chain 'J' and resid 324 through 330 Processing sheet with id=AF4, first strand: chain 'J' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG J 243 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA J 288 " --> pdb=" O GLU J 303 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 332 through 335 Processing sheet with id=AF6, first strand: chain 'K' and resid 62 through 63 Processing sheet with id=AF7, first strand: chain 'K' and resid 143 through 145 Processing sheet with id=AF8, first strand: chain 'K' and resid 324 through 330 Processing sheet with id=AF9, first strand: chain 'K' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG K 243 " --> pdb=" O THR K 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA K 288 " --> pdb=" O GLU K 303 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 332 through 335 Processing sheet with id=AG2, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AG3, first strand: chain 'L' and resid 143 through 145 Processing sheet with id=AG4, first strand: chain 'L' and resid 324 through 330 Processing sheet with id=AG5, first strand: chain 'L' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG L 243 " --> pdb=" O THR L 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 288 " --> pdb=" O GLU L 303 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 332 through 335 2676 hydrogen bonds defined for protein. 7740 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: 8.69 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15689 1.34 - 1.46: 8464 1.46 - 1.58: 22071 1.58 - 1.70: 0 1.70 - 1.82: 504 Bond restraints: 46728 Sorted by residual: bond pdb=" CB GLU G 131 " pdb=" CG GLU G 131 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB GLU K 131 " pdb=" CG GLU K 131 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB GLU H 131 " pdb=" CG GLU H 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CB GLU C 131 " pdb=" CG GLU C 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CB GLU B 131 " pdb=" CG GLU B 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 ... (remaining 46723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 61749 2.62 - 5.23: 1099 5.23 - 7.85: 92 7.85 - 10.47: 12 10.47 - 13.09: 12 Bond angle restraints: 62964 Sorted by residual: angle pdb=" C TYR G 75 " pdb=" N HIS G 76 " pdb=" CA HIS G 76 " ideal model delta sigma weight residual 122.42 116.61 5.81 1.23e+00 6.61e-01 2.23e+01 angle pdb=" C TYR D 75 " pdb=" N HIS D 76 " pdb=" CA HIS D 76 " ideal model delta sigma weight residual 122.42 116.61 5.81 1.23e+00 6.61e-01 2.23e+01 angle pdb=" C TYR H 75 " pdb=" N HIS H 76 " pdb=" CA HIS H 76 " ideal model delta sigma weight residual 122.42 116.62 5.80 1.23e+00 6.61e-01 2.22e+01 angle pdb=" C TYR B 75 " pdb=" N HIS B 76 " pdb=" CA HIS B 76 " ideal model delta sigma weight residual 122.42 116.63 5.79 1.23e+00 6.61e-01 2.21e+01 angle pdb=" C TYR L 75 " pdb=" N HIS L 76 " pdb=" CA HIS L 76 " ideal model delta sigma weight residual 122.42 116.64 5.78 1.23e+00 6.61e-01 2.21e+01 ... (remaining 62959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 27829 14.64 - 29.29: 1127 29.29 - 43.93: 120 43.93 - 58.58: 0 58.58 - 73.22: 12 Dihedral angle restraints: 29088 sinusoidal: 12216 harmonic: 16872 Sorted by residual: dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N PRO I 181 " pdb=" CA PRO I 181 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE J 180 " pdb=" C ILE J 180 " pdb=" N PRO J 181 " pdb=" CA PRO J 181 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE C 180 " pdb=" C ILE C 180 " pdb=" N PRO C 181 " pdb=" CA PRO C 181 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 29085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5448 0.059 - 0.119: 1494 0.119 - 0.178: 222 0.178 - 0.238: 12 0.238 - 0.297: 12 Chirality restraints: 7188 Sorted by residual: chirality pdb=" CB ILE D 302 " pdb=" CA ILE D 302 " pdb=" CG1 ILE D 302 " pdb=" CG2 ILE D 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE J 302 " pdb=" CA ILE J 302 " pdb=" CG1 ILE J 302 " pdb=" CG2 ILE J 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE L 302 " pdb=" CA ILE L 302 " pdb=" CG1 ILE L 302 " pdb=" CG2 ILE L 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 7185 not shown) Planarity restraints: 8172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 180 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO H 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 180 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 180 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.034 5.00e-02 4.00e+02 ... (remaining 8169 not shown) Histogram of nonbonded interaction distances: 0.30 - 1.22: 84 1.22 - 2.14: 444 2.14 - 3.06: 29190 3.06 - 3.98: 123450 3.98 - 4.90: 217594 Warning: very small nonbonded interaction distances. Nonbonded interactions: 370762 Sorted by model distance: nonbonded pdb=" CG LEU D 6 " pdb=" CB VAL E 28 " model vdw 0.296 3.900 nonbonded pdb=" CB VAL J 28 " pdb=" CG LEU L 6 " model vdw 0.297 3.900 nonbonded pdb=" CG LEU B 6 " pdb=" CB VAL K 28 " model vdw 0.297 3.900 nonbonded pdb=" CB VAL D 28 " pdb=" CG LEU G 6 " model vdw 0.297 3.900 nonbonded pdb=" CG LEU E 6 " pdb=" CB VAL G 28 " model vdw 0.297 3.900 ... (remaining 370757 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 1.160 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 32.250 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.100 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.009 0.443 46740 Z= 0.759 Angle : 0.891 13.087 62964 Z= 0.511 Chirality : 0.054 0.297 7188 Planarity : 0.007 0.061 8172 Dihedral : 8.455 73.220 18144 Min Nonbonded Distance : 0.296 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.09), residues: 5772 helix: -1.41 (0.07), residues: 3072 sheet: -1.84 (0.25), residues: 312 loop : -2.54 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 428 TYR 0.021 0.004 TYR B 96 PHE 0.023 0.003 PHE F 300 TRP 0.009 0.002 TRP A 94 HIS 0.013 0.003 HIS G 183 Details of bonding type rmsd covalent geometry : bond 0.00595 (46728) covalent geometry : angle 0.89099 (62964) hydrogen bonds : bond 0.10452 ( 2676) hydrogen bonds : angle 6.54354 ( 7740) Misc. bond : bond 0.44256 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 786 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7688 (mmm) cc_final: 0.7370 (mmm) REVERT: A 342 LEU cc_start: 0.8472 (mt) cc_final: 0.7925 (mp) REVERT: B 132 MET cc_start: 0.7641 (mmm) cc_final: 0.7122 (mmm) REVERT: B 342 LEU cc_start: 0.8316 (mt) cc_final: 0.7741 (mp) REVERT: B 485 MET cc_start: 0.5883 (ptm) cc_final: 0.5598 (ppp) REVERT: C 132 MET cc_start: 0.7623 (mmm) cc_final: 0.7183 (mmm) REVERT: C 342 LEU cc_start: 0.8540 (mt) cc_final: 0.7969 (mp) REVERT: D 15 MET cc_start: 0.8363 (ptm) cc_final: 0.8102 (ptp) REVERT: D 132 MET cc_start: 0.7705 (mmm) cc_final: 0.7391 (mmm) REVERT: D 485 MET cc_start: 0.5802 (ptm) cc_final: 0.5601 (ppp) REVERT: E 132 MET cc_start: 0.7700 (mmm) cc_final: 0.7392 (mmm) REVERT: E 342 LEU cc_start: 0.8541 (mt) cc_final: 0.8003 (mp) REVERT: E 485 MET cc_start: 0.5764 (ptm) cc_final: 0.5267 (ppp) REVERT: F 15 MET cc_start: 0.8594 (ptm) cc_final: 0.8229 (ptp) REVERT: F 132 MET cc_start: 0.7686 (mmm) cc_final: 0.7234 (mmm) REVERT: G 15 MET cc_start: 0.8484 (ptm) cc_final: 0.7840 (ptp) REVERT: H 132 MET cc_start: 0.7871 (mmm) cc_final: 0.7609 (mmm) REVERT: H 485 MET cc_start: 0.5702 (ptm) cc_final: 0.5425 (ppp) REVERT: I 15 MET cc_start: 0.8446 (ptm) cc_final: 0.8220 (ptm) REVERT: J 15 MET cc_start: 0.8331 (ptm) cc_final: 0.8077 (ptm) REVERT: J 132 MET cc_start: 0.7838 (mmm) cc_final: 0.7500 (mmm) REVERT: K 15 MET cc_start: 0.8465 (ptm) cc_final: 0.8079 (ptp) REVERT: K 132 MET cc_start: 0.7746 (mmm) cc_final: 0.7366 (mmm) REVERT: K 342 LEU cc_start: 0.8569 (mt) cc_final: 0.8057 (mp) REVERT: K 485 MET cc_start: 0.5329 (ptm) cc_final: 0.5094 (ppp) REVERT: L 15 MET cc_start: 0.8355 (ptm) cc_final: 0.8098 (ptm) REVERT: L 72 MET cc_start: 0.6204 (mmm) cc_final: 0.5973 (mmm) REVERT: L 132 MET cc_start: 0.7852 (mmm) cc_final: 0.7592 (mmm) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.2499 time to fit residues: 323.7704 Evaluate side-chains 453 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS A 316 ASN A 355 GLN B 51 ASN ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN C 51 ASN C 183 HIS C 316 ASN C 355 GLN D 51 ASN D 183 HIS ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 355 GLN E 51 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 316 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN G 51 ASN G 183 HIS G 316 ASN H 51 ASN H 183 HIS ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN I 51 ASN I 183 HIS I 316 ASN I 355 GLN J 43 HIS J 51 ASN J 183 HIS ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN J 355 GLN K 51 ASN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN L 51 ASN ** L 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS L 316 ASN L 355 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.085650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069034 restraints weight = 220311.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.070535 restraints weight = 146706.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071546 restraints weight = 110011.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.072293 restraints weight = 90045.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072787 restraints weight = 78112.944| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 46740 Z= 0.175 Angle : 0.743 11.458 62964 Z= 0.384 Chirality : 0.047 0.215 7188 Planarity : 0.006 0.060 8172 Dihedral : 5.781 24.970 6384 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.88 % Allowed : 8.27 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.11), residues: 5772 helix: 0.44 (0.09), residues: 3012 sheet: -2.48 (0.18), residues: 696 loop : -2.37 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 45 TYR 0.016 0.002 TYR F 351 PHE 0.016 0.002 PHE H 300 TRP 0.004 0.001 TRP J 94 HIS 0.004 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00391 (46728) covalent geometry : angle 0.74250 (62964) hydrogen bonds : bond 0.04423 ( 2676) hydrogen bonds : angle 5.17713 ( 7740) Misc. bond : bond 0.00892 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 500 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 MET cc_start: 0.8446 (ptm) cc_final: 0.7824 (ptm) REVERT: B 50 MET cc_start: 0.7698 (mtm) cc_final: 0.7366 (mtm) REVERT: B 222 MET cc_start: 0.6713 (mtt) cc_final: 0.6415 (mtt) REVERT: C 15 MET cc_start: 0.8372 (ptm) cc_final: 0.8068 (ptp) REVERT: D 264 MET cc_start: 0.8630 (mmm) cc_final: 0.8109 (mmt) REVERT: D 323 MET cc_start: 0.7638 (ttm) cc_final: 0.7133 (ttp) REVERT: E 222 MET cc_start: 0.6839 (mtt) cc_final: 0.6469 (mtt) REVERT: F 15 MET cc_start: 0.8257 (ptm) cc_final: 0.7938 (ptm) REVERT: F 50 MET cc_start: 0.8175 (mtm) cc_final: 0.7885 (mtm) REVERT: F 264 MET cc_start: 0.8789 (mmt) cc_final: 0.8532 (mmm) REVERT: G 50 MET cc_start: 0.8068 (mtm) cc_final: 0.7810 (mtm) REVERT: H 485 MET cc_start: 0.6586 (ptm) cc_final: 0.6339 (ppp) REVERT: J 342 LEU cc_start: 0.8209 (mt) cc_final: 0.7758 (mp) REVERT: K 15 MET cc_start: 0.8230 (ptm) cc_final: 0.7983 (ptp) REVERT: K 19 PHE cc_start: 0.7393 (t80) cc_final: 0.7093 (t80) REVERT: K 72 MET cc_start: 0.6622 (mmm) cc_final: 0.6385 (mmm) REVERT: K 485 MET cc_start: 0.6524 (ptm) cc_final: 0.6169 (ppp) REVERT: L 15 MET cc_start: 0.8163 (ptm) cc_final: 0.7860 (ptp) REVERT: L 408 MET cc_start: 0.8080 (mtt) cc_final: 0.7849 (mtt) REVERT: L 485 MET cc_start: 0.6787 (ptm) cc_final: 0.5934 (ppp) outliers start: 44 outliers final: 17 residues processed: 530 average time/residue: 0.2277 time to fit residues: 207.5769 Evaluate side-chains 423 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 406 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 133 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 453 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 484 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 510 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 295 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN C 10 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 43 HIS D 184 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 51 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN H 355 GLN ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 ASN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.083667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066701 restraints weight = 220811.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068031 restraints weight = 153200.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.068988 restraints weight = 118393.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.069637 restraints weight = 98517.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070046 restraints weight = 86702.031| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 46740 Z= 0.217 Angle : 0.704 8.938 62964 Z= 0.374 Chirality : 0.046 0.169 7188 Planarity : 0.005 0.042 8172 Dihedral : 5.619 25.361 6384 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.81 % Allowed : 10.43 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.11), residues: 5772 helix: 0.83 (0.09), residues: 3012 sheet: -2.17 (0.20), residues: 564 loop : -2.46 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 306 TYR 0.019 0.002 TYR G 351 PHE 0.021 0.002 PHE A 300 TRP 0.007 0.001 TRP G 94 HIS 0.006 0.002 HIS F 273 Details of bonding type rmsd covalent geometry : bond 0.00474 (46728) covalent geometry : angle 0.70390 (62964) hydrogen bonds : bond 0.04270 ( 2676) hydrogen bonds : angle 5.08553 ( 7740) Misc. bond : bond 0.00511 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 420 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 MET cc_start: 0.8547 (ptm) cc_final: 0.7845 (ptm) REVERT: C 15 MET cc_start: 0.8387 (ptm) cc_final: 0.8055 (ptp) REVERT: C 207 MET cc_start: 0.8557 (mmm) cc_final: 0.8163 (tpt) REVERT: D 207 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7509 (mtp) REVERT: D 485 MET cc_start: 0.7076 (ptm) cc_final: 0.5940 (tmm) REVERT: E 424 MET cc_start: 0.8408 (tmm) cc_final: 0.8190 (tmm) REVERT: F 15 MET cc_start: 0.8332 (ptm) cc_final: 0.8003 (ptm) REVERT: F 50 MET cc_start: 0.8010 (mtm) cc_final: 0.7675 (mtm) REVERT: F 125 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: F 207 MET cc_start: 0.8436 (mmm) cc_final: 0.8149 (tmm) REVERT: G 15 MET cc_start: 0.8453 (ptm) cc_final: 0.8172 (ptm) REVERT: G 22 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5702 (t80) REVERT: G 50 MET cc_start: 0.8027 (mtm) cc_final: 0.7768 (mtm) REVERT: G 207 MET cc_start: 0.8535 (mmm) cc_final: 0.8194 (mmm) REVERT: H 15 MET cc_start: 0.8433 (ptm) cc_final: 0.8207 (ptm) REVERT: I 24 MET cc_start: 0.7719 (ttm) cc_final: 0.7280 (ttm) REVERT: I 50 MET cc_start: 0.7862 (mtm) cc_final: 0.7545 (mtm) REVERT: I 195 VAL cc_start: 0.9113 (m) cc_final: 0.8847 (p) REVERT: I 207 MET cc_start: 0.8700 (mtp) cc_final: 0.8423 (tpt) REVERT: I 323 MET cc_start: 0.7001 (ttp) cc_final: 0.6755 (ttp) REVERT: I 424 MET cc_start: 0.8291 (tmm) cc_final: 0.8027 (tmm) REVERT: J 264 MET cc_start: 0.8543 (mmt) cc_final: 0.8305 (mmt) REVERT: K 15 MET cc_start: 0.8448 (ptm) cc_final: 0.8115 (ptp) REVERT: K 22 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.5466 (t80) REVERT: K 72 MET cc_start: 0.6676 (mmm) cc_final: 0.6426 (mmm) REVERT: K 207 MET cc_start: 0.8382 (mmm) cc_final: 0.7812 (tpt) REVERT: L 15 MET cc_start: 0.8193 (ptm) cc_final: 0.7816 (ptp) REVERT: L 485 MET cc_start: 0.6887 (ptm) cc_final: 0.6335 (ppp) outliers start: 91 outliers final: 23 residues processed: 495 average time/residue: 0.2313 time to fit residues: 197.5769 Evaluate side-chains 409 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 382 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 429 LEU Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 132 optimal weight: 0.9990 chunk 457 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 554 optimal weight: 9.9990 chunk 445 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 184 ASN E 10 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN I 184 ASN J 10 ASN J 43 HIS ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 355 GLN L 10 ASN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.085188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068467 restraints weight = 219299.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.069875 restraints weight = 150450.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.070849 restraints weight = 115074.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071534 restraints weight = 95181.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.071938 restraints weight = 83134.905| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46740 Z= 0.135 Angle : 0.606 7.294 62964 Z= 0.321 Chirality : 0.043 0.175 7188 Planarity : 0.004 0.042 8172 Dihedral : 5.107 20.968 6384 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.83 % Allowed : 10.33 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.11), residues: 5772 helix: 1.34 (0.09), residues: 2976 sheet: -2.20 (0.20), residues: 564 loop : -2.20 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.014 0.002 TYR I 351 PHE 0.027 0.002 PHE K 19 TRP 0.006 0.001 TRP G 93 HIS 0.003 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00295 (46728) covalent geometry : angle 0.60564 (62964) hydrogen bonds : bond 0.03795 ( 2676) hydrogen bonds : angle 4.82886 ( 7740) Misc. bond : bond 0.00540 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 421 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6659 (pt) REVERT: A 132 MET cc_start: 0.7728 (tpp) cc_final: 0.7281 (mmm) REVERT: B 15 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7837 (ptm) REVERT: B 50 MET cc_start: 0.7953 (mtm) cc_final: 0.7724 (mtm) REVERT: B 131 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: B 132 MET cc_start: 0.7359 (tpp) cc_final: 0.7080 (mmm) REVERT: C 15 MET cc_start: 0.8239 (ptm) cc_final: 0.7988 (ptp) REVERT: C 22 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5381 (t80) REVERT: C 132 MET cc_start: 0.7795 (tpp) cc_final: 0.7369 (mmm) REVERT: C 207 MET cc_start: 0.8399 (mmm) cc_final: 0.8166 (tpt) REVERT: C 222 MET cc_start: 0.6363 (mtt) cc_final: 0.6097 (mtt) REVERT: C 408 MET cc_start: 0.7770 (mmm) cc_final: 0.7454 (mmp) REVERT: D 15 MET cc_start: 0.8304 (ptm) cc_final: 0.7971 (ptp) REVERT: D 207 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7356 (mmm) REVERT: D 485 MET cc_start: 0.7282 (ptm) cc_final: 0.6178 (tmm) REVERT: E 15 MET cc_start: 0.7949 (ptp) cc_final: 0.7419 (ptm) REVERT: E 131 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: E 132 MET cc_start: 0.7553 (tpp) cc_final: 0.7122 (mmm) REVERT: F 15 MET cc_start: 0.8305 (ptm) cc_final: 0.7959 (ptm) REVERT: F 50 MET cc_start: 0.8096 (mtm) cc_final: 0.7629 (mtm) REVERT: F 207 MET cc_start: 0.8477 (mmm) cc_final: 0.8208 (mmm) REVERT: F 264 MET cc_start: 0.8571 (mmm) cc_final: 0.8275 (mmm) REVERT: F 408 MET cc_start: 0.6816 (mmm) cc_final: 0.6310 (mmm) REVERT: G 15 MET cc_start: 0.8403 (ptm) cc_final: 0.8135 (ptm) REVERT: G 207 MET cc_start: 0.8590 (mmm) cc_final: 0.8198 (mmm) REVERT: G 264 MET cc_start: 0.8635 (mmm) cc_final: 0.8372 (mmm) REVERT: H 15 MET cc_start: 0.8342 (ptm) cc_final: 0.8059 (ptm) REVERT: H 323 MET cc_start: 0.7208 (ttp) cc_final: 0.6929 (ttp) REVERT: H 426 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8419 (mm) REVERT: H 485 MET cc_start: 0.6996 (ptm) cc_final: 0.6196 (tmm) REVERT: I 24 MET cc_start: 0.7671 (ttm) cc_final: 0.7215 (ttm) REVERT: I 323 MET cc_start: 0.6904 (ttp) cc_final: 0.6675 (ttp) REVERT: I 485 MET cc_start: 0.6286 (ppp) cc_final: 0.5913 (ppp) REVERT: J 15 MET cc_start: 0.8353 (ptm) cc_final: 0.7996 (ptp) REVERT: J 264 MET cc_start: 0.8580 (mmt) cc_final: 0.8358 (mmt) REVERT: J 320 MET cc_start: 0.8590 (tpp) cc_final: 0.8337 (tpp) REVERT: J 323 MET cc_start: 0.7292 (ttp) cc_final: 0.7084 (ttp) REVERT: K 15 MET cc_start: 0.8386 (ptm) cc_final: 0.8109 (ptp) REVERT: K 24 MET cc_start: 0.7338 (mtt) cc_final: 0.7110 (mtp) REVERT: K 72 MET cc_start: 0.6787 (mmm) cc_final: 0.6533 (mmm) REVERT: K 485 MET cc_start: 0.7339 (ptm) cc_final: 0.6143 (ppp) REVERT: L 15 MET cc_start: 0.8247 (ptm) cc_final: 0.7822 (ptp) REVERT: L 207 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7894 (mmm) REVERT: L 264 MET cc_start: 0.8522 (mmm) cc_final: 0.8317 (mmm) REVERT: L 408 MET cc_start: 0.8157 (mtt) cc_final: 0.7825 (mmp) outliers start: 92 outliers final: 26 residues processed: 488 average time/residue: 0.2114 time to fit residues: 180.8077 Evaluate side-chains 418 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 384 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 186 optimal weight: 5.9990 chunk 566 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 477 optimal weight: 3.9990 chunk 512 optimal weight: 9.9990 chunk 61 optimal weight: 0.0370 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.083900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066726 restraints weight = 223510.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068090 restraints weight = 154122.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069052 restraints weight = 118971.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069696 restraints weight = 98915.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.070164 restraints weight = 87354.845| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 46740 Z= 0.193 Angle : 0.655 11.365 62964 Z= 0.349 Chirality : 0.044 0.194 7188 Planarity : 0.004 0.054 8172 Dihedral : 5.225 24.693 6384 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.59 % Allowed : 9.95 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.12), residues: 5772 helix: 1.32 (0.09), residues: 3024 sheet: -2.23 (0.20), residues: 624 loop : -2.25 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 306 TYR 0.018 0.002 TYR G 351 PHE 0.024 0.002 PHE B 19 TRP 0.009 0.001 TRP D 93 HIS 0.005 0.001 HIS I 183 Details of bonding type rmsd covalent geometry : bond 0.00424 (46728) covalent geometry : angle 0.65473 (62964) hydrogen bonds : bond 0.03952 ( 2676) hydrogen bonds : angle 4.88219 ( 7740) Misc. bond : bond 0.00497 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 393 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8032 (ptp) cc_final: 0.7689 (ptm) REVERT: A 207 MET cc_start: 0.7542 (mmm) cc_final: 0.7125 (tpt) REVERT: B 195 VAL cc_start: 0.9132 (m) cc_final: 0.8882 (p) REVERT: B 222 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6305 (mtt) REVERT: C 15 MET cc_start: 0.8363 (ptm) cc_final: 0.8064 (ptp) REVERT: C 22 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5494 (t80) REVERT: C 207 MET cc_start: 0.8579 (mmm) cc_final: 0.8275 (tpt) REVERT: C 222 MET cc_start: 0.6527 (mtt) cc_final: 0.6280 (mtt) REVERT: C 323 MET cc_start: 0.6880 (ttp) cc_final: 0.6666 (ttp) REVERT: D 15 MET cc_start: 0.8473 (ptm) cc_final: 0.8077 (ptp) REVERT: D 99 MET cc_start: 0.7037 (tpp) cc_final: 0.6648 (tpp) REVERT: D 207 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7292 (mmm) REVERT: D 485 MET cc_start: 0.7383 (ptm) cc_final: 0.6188 (ppp) REVERT: E 15 MET cc_start: 0.7855 (ptp) cc_final: 0.7653 (ptp) REVERT: E 207 MET cc_start: 0.8546 (mtp) cc_final: 0.8197 (mmm) REVERT: E 264 MET cc_start: 0.8548 (mmm) cc_final: 0.8242 (mmm) REVERT: E 424 MET cc_start: 0.8374 (tmm) cc_final: 0.8166 (tmm) REVERT: F 15 MET cc_start: 0.8477 (ptm) cc_final: 0.8113 (ptm) REVERT: F 50 MET cc_start: 0.7949 (mtm) cc_final: 0.7631 (mtm) REVERT: F 207 MET cc_start: 0.8540 (mmm) cc_final: 0.8276 (mmm) REVERT: F 264 MET cc_start: 0.8745 (mmm) cc_final: 0.8041 (mmt) REVERT: F 331 MET cc_start: 0.4703 (mmp) cc_final: 0.4409 (mmp) REVERT: F 408 MET cc_start: 0.7109 (mmm) cc_final: 0.6387 (mmm) REVERT: G 15 MET cc_start: 0.8511 (ptm) cc_final: 0.8249 (ptm) REVERT: G 22 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5921 (t80) REVERT: G 99 MET cc_start: 0.7418 (tpp) cc_final: 0.7137 (tpp) REVERT: G 264 MET cc_start: 0.8726 (mmm) cc_final: 0.8430 (mmm) REVERT: H 15 MET cc_start: 0.8393 (ptm) cc_final: 0.8061 (ptm) REVERT: H 176 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6420 (mtm) REVERT: H 485 MET cc_start: 0.7106 (ptm) cc_final: 0.6282 (tmm) REVERT: I 24 MET cc_start: 0.7749 (ttm) cc_final: 0.7340 (ttm) REVERT: I 50 MET cc_start: 0.7968 (mtm) cc_final: 0.7541 (mtm) REVERT: I 195 VAL cc_start: 0.9142 (m) cc_final: 0.8891 (p) REVERT: I 485 MET cc_start: 0.6425 (ppp) cc_final: 0.6009 (ppp) REVERT: J 15 MET cc_start: 0.8441 (ptm) cc_final: 0.8089 (ptp) REVERT: J 99 MET cc_start: 0.7157 (tpp) cc_final: 0.6788 (tpp) REVERT: J 264 MET cc_start: 0.8643 (mmt) cc_final: 0.8380 (mmt) REVERT: J 320 MET cc_start: 0.8594 (tpp) cc_final: 0.8288 (tpp) REVERT: J 323 MET cc_start: 0.7165 (ttp) cc_final: 0.6962 (ttp) REVERT: J 408 MET cc_start: 0.7418 (mmt) cc_final: 0.6814 (mmm) REVERT: K 15 MET cc_start: 0.8554 (ptm) cc_final: 0.8183 (ptp) REVERT: K 22 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5659 (t80) REVERT: K 24 MET cc_start: 0.7438 (mtt) cc_final: 0.7174 (mtp) REVERT: K 72 MET cc_start: 0.6661 (mmm) cc_final: 0.6344 (mmm) REVERT: K 207 MET cc_start: 0.8305 (mmm) cc_final: 0.8009 (tpt) REVERT: K 264 MET cc_start: 0.8541 (mmm) cc_final: 0.8305 (mmm) REVERT: K 331 MET cc_start: 0.4739 (mmp) cc_final: 0.4443 (mmp) REVERT: K 485 MET cc_start: 0.7378 (ptm) cc_final: 0.6399 (tmm) REVERT: L 15 MET cc_start: 0.8340 (ptm) cc_final: 0.7863 (ptp) outliers start: 130 outliers final: 66 residues processed: 495 average time/residue: 0.2591 time to fit residues: 222.8765 Evaluate side-chains 450 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 376 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 497 optimal weight: 0.1980 chunk 434 optimal weight: 0.0980 chunk 562 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 405 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.086653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.070074 restraints weight = 217571.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.071591 restraints weight = 145951.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072660 restraints weight = 109541.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.073386 restraints weight = 89206.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073865 restraints weight = 77296.516| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 46740 Z= 0.111 Angle : 0.583 9.943 62964 Z= 0.307 Chirality : 0.043 0.198 7188 Planarity : 0.004 0.038 8172 Dihedral : 4.746 22.919 6384 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.83 % Allowed : 10.87 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.12), residues: 5772 helix: 1.58 (0.10), residues: 3012 sheet: -1.85 (0.21), residues: 552 loop : -2.23 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 306 TYR 0.016 0.002 TYR J 231 PHE 0.036 0.001 PHE K 19 TRP 0.011 0.001 TRP D 93 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00247 (46728) covalent geometry : angle 0.58280 (62964) hydrogen bonds : bond 0.03551 ( 2676) hydrogen bonds : angle 4.67570 ( 7740) Misc. bond : bond 0.00484 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 409 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 MET cc_start: 0.7105 (ttm) cc_final: 0.6803 (ttm) REVERT: B 485 MET cc_start: 0.6820 (ppp) cc_final: 0.6391 (ppp) REVERT: C 15 MET cc_start: 0.8138 (ptm) cc_final: 0.7424 (ptp) REVERT: C 22 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.5149 (t80) REVERT: C 207 MET cc_start: 0.8477 (mmm) cc_final: 0.8220 (mmm) REVERT: C 323 MET cc_start: 0.6852 (ttp) cc_final: 0.6608 (ttp) REVERT: C 485 MET cc_start: 0.6343 (ppp) cc_final: 0.5942 (ppp) REVERT: D 15 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (ptp) REVERT: D 99 MET cc_start: 0.6932 (tpp) cc_final: 0.6605 (tpp) REVERT: D 207 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7225 (mmm) REVERT: D 485 MET cc_start: 0.7607 (ptm) cc_final: 0.6725 (ppp) REVERT: E 15 MET cc_start: 0.7780 (ptp) cc_final: 0.7500 (ptp) REVERT: E 207 MET cc_start: 0.8307 (mtp) cc_final: 0.7954 (tpt) REVERT: E 264 MET cc_start: 0.8629 (mmm) cc_final: 0.8341 (mmm) REVERT: E 408 MET cc_start: 0.6803 (mmt) cc_final: 0.6462 (mmm) REVERT: E 424 MET cc_start: 0.8384 (tmm) cc_final: 0.8155 (tmm) REVERT: E 485 MET cc_start: 0.6817 (ppp) cc_final: 0.6587 (ppp) REVERT: F 15 MET cc_start: 0.8228 (ptm) cc_final: 0.7912 (ptm) REVERT: F 50 MET cc_start: 0.8005 (mtm) cc_final: 0.7506 (mtm) REVERT: F 264 MET cc_start: 0.8677 (mmm) cc_final: 0.8105 (mmt) REVERT: F 408 MET cc_start: 0.7230 (mmm) cc_final: 0.6648 (mmm) REVERT: F 485 MET cc_start: 0.6375 (ppp) cc_final: 0.6119 (ppp) REVERT: G 22 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5764 (t80) REVERT: G 99 MET cc_start: 0.7309 (tpp) cc_final: 0.6767 (tpp) REVERT: G 207 MET cc_start: 0.8519 (mmm) cc_final: 0.8250 (mmm) REVERT: G 264 MET cc_start: 0.8735 (mmm) cc_final: 0.8031 (mmt) REVERT: G 408 MET cc_start: 0.7277 (mmt) cc_final: 0.6706 (mmm) REVERT: H 15 MET cc_start: 0.8270 (ptm) cc_final: 0.7962 (ptm) REVERT: H 222 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6350 (mtt) REVERT: I 24 MET cc_start: 0.7702 (ttm) cc_final: 0.7302 (ttm) REVERT: I 207 MET cc_start: 0.8628 (mtp) cc_final: 0.8306 (tpt) REVERT: I 408 MET cc_start: 0.7445 (mmt) cc_final: 0.7028 (mmp) REVERT: J 15 MET cc_start: 0.8351 (ptm) cc_final: 0.8006 (ptm) REVERT: J 99 MET cc_start: 0.6920 (tpp) cc_final: 0.6573 (tpp) REVERT: J 207 MET cc_start: 0.7534 (tpt) cc_final: 0.7299 (mmm) REVERT: J 408 MET cc_start: 0.7188 (mmt) cc_final: 0.6686 (mmm) REVERT: K 15 MET cc_start: 0.8277 (ptm) cc_final: 0.8053 (ptp) REVERT: K 22 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5404 (t80) REVERT: K 24 MET cc_start: 0.7441 (mtt) cc_final: 0.7193 (mtp) REVERT: K 72 MET cc_start: 0.6781 (mmm) cc_final: 0.6519 (mmm) REVERT: K 264 MET cc_start: 0.8711 (mmm) cc_final: 0.8450 (mmm) REVERT: K 485 MET cc_start: 0.7233 (ptm) cc_final: 0.6012 (ppp) REVERT: L 15 MET cc_start: 0.8344 (ptm) cc_final: 0.8061 (ptm) REVERT: L 485 MET cc_start: 0.7162 (ptm) cc_final: 0.6852 (ppp) outliers start: 92 outliers final: 52 residues processed: 470 average time/residue: 0.2543 time to fit residues: 207.4519 Evaluate side-chains 449 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 391 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 99 optimal weight: 3.9990 chunk 483 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 76 optimal weight: 40.0000 chunk 185 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 391 optimal weight: 0.0060 chunk 272 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 545 optimal weight: 8.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.085022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068078 restraints weight = 221687.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069469 restraints weight = 150691.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070452 restraints weight = 115117.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.071129 restraints weight = 95249.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.071549 restraints weight = 83471.749| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46740 Z= 0.158 Angle : 0.632 10.934 62964 Z= 0.332 Chirality : 0.044 0.181 7188 Planarity : 0.004 0.036 8172 Dihedral : 4.887 24.332 6384 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.27 % Allowed : 11.06 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.12), residues: 5772 helix: 1.59 (0.10), residues: 3060 sheet: -1.83 (0.21), residues: 612 loop : -2.18 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.015 0.002 TYR B 351 PHE 0.022 0.002 PHE B 19 TRP 0.006 0.001 TRP D 93 HIS 0.003 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00352 (46728) covalent geometry : angle 0.63220 (62964) hydrogen bonds : bond 0.03734 ( 2676) hydrogen bonds : angle 4.70467 ( 7740) Misc. bond : bond 0.00455 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 397 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 MET cc_start: 0.8074 (ptp) cc_final: 0.7823 (ptm) REVERT: B 323 MET cc_start: 0.7197 (ttm) cc_final: 0.6888 (ttm) REVERT: B 408 MET cc_start: 0.7693 (mmt) cc_final: 0.6963 (mmm) REVERT: B 485 MET cc_start: 0.6799 (ppp) cc_final: 0.6193 (ppp) REVERT: C 22 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5374 (t80) REVERT: C 176 MET cc_start: 0.6827 (mtm) cc_final: 0.6626 (mtm) REVERT: C 195 VAL cc_start: 0.9065 (m) cc_final: 0.8833 (p) REVERT: C 207 MET cc_start: 0.8646 (mmm) cc_final: 0.8228 (tpt) REVERT: C 323 MET cc_start: 0.6895 (ttp) cc_final: 0.6638 (ttp) REVERT: D 15 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8126 (ptp) REVERT: D 99 MET cc_start: 0.7113 (tpp) cc_final: 0.6791 (tpp) REVERT: D 207 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7264 (mmm) REVERT: D 485 MET cc_start: 0.7489 (ptm) cc_final: 0.6514 (ppp) REVERT: E 264 MET cc_start: 0.8702 (mmm) cc_final: 0.8410 (mmm) REVERT: E 408 MET cc_start: 0.7032 (mmt) cc_final: 0.6712 (mmm) REVERT: E 424 MET cc_start: 0.8439 (tmm) cc_final: 0.8190 (tmm) REVERT: E 450 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7582 (t70) REVERT: F 15 MET cc_start: 0.8369 (ptm) cc_final: 0.8031 (ptm) REVERT: F 50 MET cc_start: 0.7858 (mtm) cc_final: 0.7531 (mtm) REVERT: F 264 MET cc_start: 0.8747 (mmm) cc_final: 0.8099 (mmt) REVERT: F 408 MET cc_start: 0.7499 (mmm) cc_final: 0.7279 (mmm) REVERT: F 485 MET cc_start: 0.6279 (ppp) cc_final: 0.6061 (ppp) REVERT: G 22 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5987 (t80) REVERT: G 99 MET cc_start: 0.7347 (tpp) cc_final: 0.7007 (tpp) REVERT: G 207 MET cc_start: 0.8580 (mmm) cc_final: 0.8320 (mmm) REVERT: H 15 MET cc_start: 0.8232 (ptm) cc_final: 0.7884 (ptm) REVERT: H 176 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6420 (mtm) REVERT: H 207 MET cc_start: 0.8311 (mmm) cc_final: 0.7904 (mmm) REVERT: H 222 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6488 (mtt) REVERT: I 24 MET cc_start: 0.7753 (ttm) cc_final: 0.7378 (ttm) REVERT: I 50 MET cc_start: 0.7873 (mtm) cc_final: 0.7347 (mtm) REVERT: I 485 MET cc_start: 0.6287 (ppp) cc_final: 0.5822 (ppp) REVERT: J 15 MET cc_start: 0.8414 (ptm) cc_final: 0.7954 (ptm) REVERT: J 99 MET cc_start: 0.7202 (tpp) cc_final: 0.6901 (tpp) REVERT: J 207 MET cc_start: 0.7648 (tpt) cc_final: 0.7304 (mmm) REVERT: J 485 MET cc_start: 0.6552 (ppp) cc_final: 0.5922 (ppp) REVERT: K 15 MET cc_start: 0.8383 (ptm) cc_final: 0.8097 (ptp) REVERT: K 22 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5455 (t80) REVERT: K 24 MET cc_start: 0.7393 (mtt) cc_final: 0.7108 (mtp) REVERT: K 72 MET cc_start: 0.6705 (mmm) cc_final: 0.6413 (mmm) REVERT: K 408 MET cc_start: 0.7430 (mmt) cc_final: 0.6884 (mmm) REVERT: K 485 MET cc_start: 0.7267 (ptm) cc_final: 0.6110 (ppp) REVERT: L 15 MET cc_start: 0.8409 (ptm) cc_final: 0.8094 (ptm) REVERT: L 408 MET cc_start: 0.7199 (mmm) cc_final: 0.6911 (mmm) REVERT: L 485 MET cc_start: 0.7131 (ptm) cc_final: 0.5894 (ppp) outliers start: 114 outliers final: 69 residues processed: 485 average time/residue: 0.2286 time to fit residues: 192.1159 Evaluate side-chains 463 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 386 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 450 ASP Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 381 optimal weight: 8.9990 chunk 452 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 553 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN K 5 ASN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.083267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065557 restraints weight = 221369.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066898 restraints weight = 151761.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067823 restraints weight = 116634.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068459 restraints weight = 97176.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068894 restraints weight = 85738.896| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 46740 Z= 0.267 Angle : 0.774 12.861 62964 Z= 0.406 Chirality : 0.047 0.255 7188 Planarity : 0.005 0.047 8172 Dihedral : 5.526 28.583 6384 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.65 % Allowed : 10.94 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.11), residues: 5772 helix: 1.24 (0.09), residues: 3012 sheet: -1.72 (0.22), residues: 552 loop : -2.13 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 306 TYR 0.020 0.003 TYR F 351 PHE 0.030 0.003 PHE B 19 TRP 0.010 0.001 TRP G 94 HIS 0.005 0.002 HIS I 183 Details of bonding type rmsd covalent geometry : bond 0.00581 (46728) covalent geometry : angle 0.77413 (62964) hydrogen bonds : bond 0.04303 ( 2676) hydrogen bonds : angle 5.06311 ( 7740) Misc. bond : bond 0.00504 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 385 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.7704 (ppp) cc_final: 0.7473 (ppp) REVERT: B 408 MET cc_start: 0.7709 (mmt) cc_final: 0.7097 (mmm) REVERT: B 432 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 485 MET cc_start: 0.6877 (ppp) cc_final: 0.6628 (ppp) REVERT: C 22 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.5701 (t80) REVERT: C 195 VAL cc_start: 0.9160 (m) cc_final: 0.8925 (p) REVERT: C 207 MET cc_start: 0.8532 (mmm) cc_final: 0.8254 (tpt) REVERT: C 408 MET cc_start: 0.7243 (mmp) cc_final: 0.6842 (mmp) REVERT: D 15 MET cc_start: 0.8499 (ptm) cc_final: 0.8177 (ptp) REVERT: D 222 MET cc_start: 0.6627 (mtt) cc_final: 0.6212 (mpp) REVERT: D 485 MET cc_start: 0.7783 (ptm) cc_final: 0.6754 (ppp) REVERT: E 408 MET cc_start: 0.7385 (mmt) cc_final: 0.6654 (mmp) REVERT: E 424 MET cc_start: 0.8522 (tmm) cc_final: 0.8309 (tmm) REVERT: F 15 MET cc_start: 0.8490 (ptm) cc_final: 0.8138 (ptm) REVERT: F 50 MET cc_start: 0.7929 (mtm) cc_final: 0.7630 (mtm) REVERT: F 207 MET cc_start: 0.8659 (mtp) cc_final: 0.8387 (mmm) REVERT: F 264 MET cc_start: 0.8800 (mmm) cc_final: 0.8174 (mmt) REVERT: G 15 MET cc_start: 0.8328 (ptm) cc_final: 0.8078 (ptm) REVERT: G 22 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.6056 (t80) REVERT: G 99 MET cc_start: 0.7355 (tpp) cc_final: 0.7140 (mmt) REVERT: G 408 MET cc_start: 0.7384 (mmt) cc_final: 0.6964 (mmm) REVERT: H 15 MET cc_start: 0.8400 (ptm) cc_final: 0.8026 (ptm) REVERT: H 176 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6606 (mtm) REVERT: H 207 MET cc_start: 0.8215 (mmm) cc_final: 0.7924 (mmm) REVERT: H 222 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6256 (mtt) REVERT: H 408 MET cc_start: 0.7614 (mmt) cc_final: 0.6918 (mmm) REVERT: H 485 MET cc_start: 0.7375 (ptm) cc_final: 0.6877 (ppp) REVERT: I 50 MET cc_start: 0.7886 (mtm) cc_final: 0.7495 (mtm) REVERT: I 264 MET cc_start: 0.8673 (mmm) cc_final: 0.8444 (mmm) REVERT: I 485 MET cc_start: 0.6483 (ppp) cc_final: 0.6234 (ppp) REVERT: J 15 MET cc_start: 0.8505 (ptm) cc_final: 0.8057 (ptp) REVERT: J 99 MET cc_start: 0.7663 (tpp) cc_final: 0.7284 (tpp) REVERT: J 408 MET cc_start: 0.7514 (mmt) cc_final: 0.6733 (mmm) REVERT: J 485 MET cc_start: 0.6758 (ppp) cc_final: 0.6162 (ppp) REVERT: K 15 MET cc_start: 0.8583 (ptm) cc_final: 0.8199 (ptp) REVERT: K 22 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.5797 (t80) REVERT: K 24 MET cc_start: 0.7483 (mtt) cc_final: 0.7229 (mtp) REVERT: K 485 MET cc_start: 0.7353 (ptm) cc_final: 0.6456 (tmm) REVERT: L 15 MET cc_start: 0.8485 (ptm) cc_final: 0.8128 (ptm) REVERT: L 408 MET cc_start: 0.7662 (mmm) cc_final: 0.7423 (mmm) REVERT: L 485 MET cc_start: 0.7717 (ptm) cc_final: 0.7487 (ppp) outliers start: 133 outliers final: 89 residues processed: 488 average time/residue: 0.2213 time to fit residues: 186.3760 Evaluate side-chains 465 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 370 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 450 ASP Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 402 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 559 optimal weight: 5.9990 chunk 505 optimal weight: 8.9990 chunk 411 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 567 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 546 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.085178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068222 restraints weight = 218239.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.069608 restraints weight = 149667.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.070589 restraints weight = 114375.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071197 restraints weight = 94693.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.071690 restraints weight = 83406.567| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 46740 Z= 0.150 Angle : 0.678 13.937 62964 Z= 0.349 Chirality : 0.045 0.221 7188 Planarity : 0.004 0.065 8172 Dihedral : 5.083 25.550 6384 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.17 % Allowed : 11.92 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.12), residues: 5772 helix: 1.41 (0.10), residues: 3060 sheet: -1.70 (0.22), residues: 552 loop : -2.12 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 306 TYR 0.015 0.002 TYR F 351 PHE 0.036 0.002 PHE K 19 TRP 0.015 0.001 TRP K 93 HIS 0.004 0.001 HIS L 228 Details of bonding type rmsd covalent geometry : bond 0.00344 (46728) covalent geometry : angle 0.67759 (62964) hydrogen bonds : bond 0.03780 ( 2676) hydrogen bonds : angle 4.83786 ( 7740) Misc. bond : bond 0.00650 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 393 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.7546 (ppp) cc_final: 0.7260 (ppp) REVERT: B 323 MET cc_start: 0.7254 (ttm) cc_final: 0.6924 (ttm) REVERT: B 408 MET cc_start: 0.7682 (mmt) cc_final: 0.7177 (mmm) REVERT: B 432 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7130 (mp) REVERT: C 6 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6752 (pt) REVERT: C 22 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5361 (t80) REVERT: C 207 MET cc_start: 0.8611 (mmm) cc_final: 0.8316 (tpt) REVERT: C 408 MET cc_start: 0.7125 (mmp) cc_final: 0.6673 (mmp) REVERT: D 15 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8091 (ptp) REVERT: D 485 MET cc_start: 0.8050 (ptm) cc_final: 0.6988 (ppp) REVERT: E 408 MET cc_start: 0.7127 (mmt) cc_final: 0.6772 (mmm) REVERT: E 424 MET cc_start: 0.8496 (tmm) cc_final: 0.8253 (tmm) REVERT: F 15 MET cc_start: 0.8287 (ptm) cc_final: 0.7940 (ptm) REVERT: F 50 MET cc_start: 0.7988 (mtm) cc_final: 0.7496 (mtm) REVERT: F 207 MET cc_start: 0.8627 (mtp) cc_final: 0.8309 (tmm) REVERT: F 264 MET cc_start: 0.8787 (mmm) cc_final: 0.8214 (mmt) REVERT: F 485 MET cc_start: 0.6342 (ppp) cc_final: 0.6072 (ppp) REVERT: G 15 MET cc_start: 0.8323 (ptm) cc_final: 0.8073 (ptm) REVERT: G 22 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5860 (t80) REVERT: G 99 MET cc_start: 0.7321 (tpp) cc_final: 0.7059 (tpp) REVERT: H 15 MET cc_start: 0.8182 (ptm) cc_final: 0.7800 (ptm) REVERT: H 176 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6442 (mtm) REVERT: H 207 MET cc_start: 0.8296 (mmm) cc_final: 0.7971 (mmm) REVERT: H 222 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6495 (mtt) REVERT: H 408 MET cc_start: 0.7449 (mmt) cc_final: 0.6732 (mmm) REVERT: I 24 MET cc_start: 0.7573 (ttm) cc_final: 0.7314 (ttm) REVERT: I 50 MET cc_start: 0.7868 (mtm) cc_final: 0.7337 (mtm) REVERT: I 264 MET cc_start: 0.8705 (mmm) cc_final: 0.8472 (mmm) REVERT: I 485 MET cc_start: 0.6368 (ppp) cc_final: 0.6163 (ppp) REVERT: J 15 MET cc_start: 0.8361 (ptm) cc_final: 0.8012 (ptm) REVERT: J 99 MET cc_start: 0.7323 (tpp) cc_final: 0.6982 (tpp) REVERT: J 264 MET cc_start: 0.8680 (mmt) cc_final: 0.8219 (mmt) REVERT: J 408 MET cc_start: 0.7409 (mmt) cc_final: 0.6591 (mmm) REVERT: J 485 MET cc_start: 0.6749 (ppp) cc_final: 0.6224 (ppp) REVERT: K 15 MET cc_start: 0.8350 (ptm) cc_final: 0.8085 (ptp) REVERT: K 22 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5413 (t80) REVERT: K 24 MET cc_start: 0.7433 (mtt) cc_final: 0.7164 (mtp) REVERT: K 72 MET cc_start: 0.6862 (mmm) cc_final: 0.6656 (mmm) REVERT: K 99 MET cc_start: 0.7289 (tpp) cc_final: 0.6909 (mmm) REVERT: K 207 MET cc_start: 0.8387 (mmm) cc_final: 0.8087 (tpt) REVERT: K 408 MET cc_start: 0.7381 (mmt) cc_final: 0.6845 (mmm) REVERT: K 485 MET cc_start: 0.7323 (ptm) cc_final: 0.6105 (ppp) REVERT: L 15 MET cc_start: 0.8334 (ptm) cc_final: 0.7975 (ptm) REVERT: L 207 MET cc_start: 0.8261 (tpp) cc_final: 0.7886 (mmm) REVERT: L 485 MET cc_start: 0.7643 (ptm) cc_final: 0.7359 (ppp) outliers start: 109 outliers final: 77 residues processed: 475 average time/residue: 0.2221 time to fit residues: 183.5897 Evaluate side-chains 464 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 379 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 392 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 490 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 487 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN C 10 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.085795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068821 restraints weight = 220194.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070198 restraints weight = 149981.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071185 restraints weight = 114816.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.071850 restraints weight = 95051.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.072222 restraints weight = 83441.963| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 46740 Z= 0.144 Angle : 0.675 13.801 62964 Z= 0.344 Chirality : 0.045 0.309 7188 Planarity : 0.004 0.051 8172 Dihedral : 4.947 25.448 6384 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.85 % Allowed : 12.26 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.12), residues: 5772 helix: 1.65 (0.10), residues: 3048 sheet: -1.59 (0.22), residues: 552 loop : -2.03 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 306 TYR 0.015 0.002 TYR D 263 PHE 0.017 0.002 PHE B 19 TRP 0.010 0.001 TRP K 93 HIS 0.003 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00332 (46728) covalent geometry : angle 0.67521 (62964) hydrogen bonds : bond 0.03727 ( 2676) hydrogen bonds : angle 4.79013 ( 7740) Misc. bond : bond 0.00708 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 396 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8017 (ppp) cc_final: 0.7584 (ppp) REVERT: A 485 MET cc_start: 0.7578 (ppp) cc_final: 0.7341 (ppp) REVERT: B 264 MET cc_start: 0.8711 (mmt) cc_final: 0.8412 (mmm) REVERT: B 323 MET cc_start: 0.7190 (ttm) cc_final: 0.6886 (ttm) REVERT: B 408 MET cc_start: 0.7597 (mmt) cc_final: 0.7138 (mmm) REVERT: B 432 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7144 (mp) REVERT: B 485 MET cc_start: 0.7006 (ppp) cc_final: 0.6547 (ppp) REVERT: C 22 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5356 (t80) REVERT: C 207 MET cc_start: 0.8612 (mmm) cc_final: 0.8325 (tpt) REVERT: C 264 MET cc_start: 0.8788 (mmt) cc_final: 0.8529 (mmt) REVERT: C 485 MET cc_start: 0.6243 (ppp) cc_final: 0.6035 (ppp) REVERT: D 132 MET cc_start: 0.7316 (mmm) cc_final: 0.6967 (tpp) REVERT: D 408 MET cc_start: 0.7527 (mmt) cc_final: 0.6933 (mmp) REVERT: D 485 MET cc_start: 0.7854 (ptm) cc_final: 0.6873 (ppp) REVERT: E 408 MET cc_start: 0.7092 (mmt) cc_final: 0.6625 (mmm) REVERT: E 424 MET cc_start: 0.8485 (tmm) cc_final: 0.8274 (tmm) REVERT: E 450 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7542 (t70) REVERT: F 15 MET cc_start: 0.8214 (ptm) cc_final: 0.7852 (ptm) REVERT: F 50 MET cc_start: 0.7924 (mtm) cc_final: 0.7494 (mtm) REVERT: F 207 MET cc_start: 0.8587 (mtp) cc_final: 0.8278 (mmm) REVERT: F 264 MET cc_start: 0.8805 (mmm) cc_final: 0.8233 (mmt) REVERT: F 485 MET cc_start: 0.6543 (ppp) cc_final: 0.6251 (ppp) REVERT: G 15 MET cc_start: 0.8194 (ptm) cc_final: 0.7917 (ptm) REVERT: G 22 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5912 (t80) REVERT: G 99 MET cc_start: 0.7318 (tpp) cc_final: 0.7077 (tpp) REVERT: G 408 MET cc_start: 0.7040 (mmt) cc_final: 0.6489 (mmm) REVERT: H 15 MET cc_start: 0.8263 (ptm) cc_final: 0.7957 (ptm) REVERT: H 207 MET cc_start: 0.8316 (mmm) cc_final: 0.7973 (mmm) REVERT: H 222 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6486 (mtt) REVERT: H 320 MET cc_start: 0.8565 (tpp) cc_final: 0.8191 (tpp) REVERT: H 408 MET cc_start: 0.7341 (mmt) cc_final: 0.6693 (mmm) REVERT: I 24 MET cc_start: 0.7495 (ttm) cc_final: 0.7258 (ttm) REVERT: I 50 MET cc_start: 0.7876 (mtm) cc_final: 0.7359 (mtm) REVERT: I 264 MET cc_start: 0.8713 (mmm) cc_final: 0.8473 (mmm) REVERT: J 6 LEU cc_start: 0.7011 (mt) cc_final: 0.6789 (pt) REVERT: J 15 MET cc_start: 0.8380 (ptm) cc_final: 0.8034 (ptm) REVERT: J 99 MET cc_start: 0.7330 (tpp) cc_final: 0.6970 (tpp) REVERT: J 264 MET cc_start: 0.8662 (mmt) cc_final: 0.8242 (mmt) REVERT: J 408 MET cc_start: 0.7320 (mmt) cc_final: 0.6512 (mmm) REVERT: J 485 MET cc_start: 0.6706 (ppp) cc_final: 0.6145 (ppp) REVERT: K 15 MET cc_start: 0.8316 (ptm) cc_final: 0.8036 (ptp) REVERT: K 22 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5307 (t80) REVERT: K 72 MET cc_start: 0.6877 (mmm) cc_final: 0.6657 (mmm) REVERT: K 99 MET cc_start: 0.7199 (tpp) cc_final: 0.6780 (mmm) REVERT: K 207 MET cc_start: 0.8436 (mmm) cc_final: 0.8080 (tpt) REVERT: K 485 MET cc_start: 0.7423 (ptm) cc_final: 0.6851 (tmm) REVERT: L 15 MET cc_start: 0.8424 (ptm) cc_final: 0.8029 (ptm) REVERT: L 207 MET cc_start: 0.8249 (tpp) cc_final: 0.7888 (mmm) REVERT: L 306 ARG cc_start: 0.6211 (mmm160) cc_final: 0.5942 (mmm160) REVERT: L 408 MET cc_start: 0.6818 (mmm) cc_final: 0.6441 (mmm) REVERT: L 485 MET cc_start: 0.7770 (ptm) cc_final: 0.7542 (ppp) outliers start: 93 outliers final: 71 residues processed: 467 average time/residue: 0.2210 time to fit residues: 178.4874 Evaluate side-chains 462 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 385 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 353 optimal weight: 4.9990 chunk 481 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 519 optimal weight: 6.9990 chunk 356 optimal weight: 0.7980 chunk 374 optimal weight: 20.0000 chunk 439 optimal weight: 3.9990 chunk 431 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.085353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068161 restraints weight = 219175.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069572 restraints weight = 149655.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.070479 restraints weight = 114453.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.071196 restraints weight = 95389.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.071641 restraints weight = 83703.126| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 46740 Z= 0.161 Angle : 0.686 14.294 62964 Z= 0.352 Chirality : 0.045 0.292 7188 Planarity : 0.004 0.048 8172 Dihedral : 4.993 26.037 6384 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.87 % Allowed : 12.24 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.12), residues: 5772 helix: 1.64 (0.10), residues: 3060 sheet: -1.70 (0.22), residues: 612 loop : -2.05 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 306 TYR 0.016 0.002 TYR C 75 PHE 0.020 0.002 PHE B 19 TRP 0.007 0.001 TRP K 93 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00366 (46728) covalent geometry : angle 0.68620 (62964) hydrogen bonds : bond 0.03779 ( 2676) hydrogen bonds : angle 4.80570 ( 7740) Misc. bond : bond 0.00708 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7524.50 seconds wall clock time: 130 minutes 50.05 seconds (7850.05 seconds total)