Starting phenix.real_space_refine on Sat Dec 28 19:43:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoj_33349/12_2024/7xoj_33349.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 280 5.16 5 C 33558 2.51 5 N 9310 2.21 5 O 10822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 53970 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 23.39, per 1000 atoms: 0.43 Number of scatterers: 53970 At special positions: 0 Unit cell: (155.73, 159.21, 156.6, 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 280 16.00 O 10822 8.00 N 9310 7.00 C 33558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.76 Conformation dependent library (CDL) restraints added in 5.7 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 84 sheets defined 59.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.139A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.546A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.512A pdb=" N PHE A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.881A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.009A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.232A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 110 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.613A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 244 removed outlier: 4.417A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.542A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.948A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.129A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 86 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.578A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.805A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.184A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.561A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.506A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.593A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 removed outlier: 3.665A pdb=" N GLU D 232 " --> pdb=" O ASN D 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.931A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.249A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.573A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.614A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 244 removed outlier: 4.380A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 427 removed outlier: 4.076A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 458 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 4.335A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.569A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.570A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 427 removed outlier: 4.111A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 458 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.067A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'G' and resid 64 through 86 Processing helix chain 'G' and resid 88 through 110 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.642A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 4.208A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.867A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 458 Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 4.211A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.592A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 338 through 356 removed outlier: 3.502A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 375 removed outlier: 4.385A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.903A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 458 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.161A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 86 Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.614A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.783A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA I 260 " --> pdb=" O GLY I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 removed outlier: 4.265A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 removed outlier: 3.815A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 458 Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 461 through 472 removed outlier: 3.507A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.066A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.509A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.637A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 244 removed outlier: 4.306A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 427 removed outlier: 3.876A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 458 Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.192A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.546A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.569A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 244 removed outlier: 4.377A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.929A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 458 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.160A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.561A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.549A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 244 removed outlier: 4.442A pdb=" N MET L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 338 through 356 removed outlier: 3.539A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 427 removed outlier: 3.949A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 458 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 29 removed outlier: 4.136A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.557A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.558A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 232 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.788A pdb=" N ILE M 342 " --> pdb=" O GLU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 removed outlier: 4.210A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 427 removed outlier: 4.068A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 458 Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.051A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 88 through 110 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.640A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 232 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 256 through 269 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 338 through 356 removed outlier: 3.592A pdb=" N ILE N 342 " --> pdb=" O GLU N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 374 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.845A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 458 Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.457A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.381A pdb=" N ASN A 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS B 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.195A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 8.466A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.532A pdb=" N GLU A 484 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.036A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 7 " --> pdb=" O MET C 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.489A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.161A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.161A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.958A pdb=" N ASN C 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL D 521 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ASP D 523 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.492A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.205A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.205A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 removed outlier: 3.515A pdb=" N GLU C 484 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.358A pdb=" N ASN D 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS E 519 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.383A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.383A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 479 removed outlier: 3.588A pdb=" N GLU D 484 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.890A pdb=" N ASN E 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL F 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ASP F 523 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.265A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.265A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 251 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.642A pdb=" N GLU E 484 " --> pdb=" O ASN E 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.927A pdb=" N ASN F 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL G 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL F 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ASP G 523 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AD7, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.607A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.607A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'F' and resid 476 through 479 removed outlier: 3.581A pdb=" N GLU F 484 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AE3, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.230A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.230A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'G' and resid 476 through 479 removed outlier: 3.647A pdb=" N GLU G 484 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.407A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS H 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.437A pdb=" N ASN H 37 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS I 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.517A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.195A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 213 through 216 removed outlier: 8.538A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'H' and resid 476 through 479 removed outlier: 3.530A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.952A pdb=" N ASN I 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N VAL J 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL I 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP J 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AF7, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.273A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 213 through 216 removed outlier: 8.322A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG1, first strand: chain 'I' and resid 476 through 479 removed outlier: 3.619A pdb=" N GLU I 484 " --> pdb=" O ASN I 479 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.992A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG4, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.230A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 213 through 216 removed outlier: 8.494A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AG8, first strand: chain 'K' and resid 48 through 50 removed outlier: 6.454A pdb=" N ASN K 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS L 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AH1, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.245A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 213 through 216 removed outlier: 8.464A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'K' and resid 476 through 479 removed outlier: 3.556A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.850A pdb=" N ASN L 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL M 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL L 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ASP M 523 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AH7, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.159A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.159A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'L' and resid 476 through 479 removed outlier: 3.528A pdb=" N GLU L 484 " --> pdb=" O ASN L 479 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.811A pdb=" N ASN M 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL N 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL M 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ASP N 523 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.508A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 193 through 195 Processing sheet with id=AI5, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.961A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'M' and resid 476 through 479 removed outlier: 3.591A pdb=" N GLU M 484 " --> pdb=" O ASN M 479 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.497A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.239A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.239A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 3817 hydrogen bonds defined for protein. 11019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.80 Time building geometry restraints manager: 12.61 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: 18739 1.34 - 1.46: 9047 1.46 - 1.58: 26058 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 54362 Sorted by residual: bond pdb=" CB MET B 16 " pdb=" CG MET B 16 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" SD MET E 520 " pdb=" CE MET E 520 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" SD MET C 520 " pdb=" CE MET C 520 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" SD MET L 520 " pdb=" CE MET L 520 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA MET L 520 " pdb=" CB MET L 520 " ideal model delta sigma weight residual 1.535 1.512 0.023 1.90e-02 2.77e+03 1.50e+00 ... (remaining 54357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 72480 1.69 - 3.38: 770 3.38 - 5.07: 124 5.07 - 6.76: 18 6.76 - 8.46: 10 Bond angle restraints: 73402 Sorted by residual: angle pdb=" CB ARG H 350 " pdb=" CG ARG H 350 " pdb=" CD ARG H 350 " ideal model delta sigma weight residual 111.30 119.76 -8.46 2.30e+00 1.89e-01 1.35e+01 angle pdb=" N GLU N 354 " pdb=" CA GLU N 354 " pdb=" CB GLU N 354 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLU B 354 " pdb=" CA GLU B 354 " pdb=" CB GLU B 354 " ideal model delta sigma weight residual 110.20 115.09 -4.89 1.49e+00 4.50e-01 1.08e+01 angle pdb=" C ALA G 163 " pdb=" N GLU G 164 " pdb=" CA GLU G 164 " ideal model delta sigma weight residual 120.72 115.29 5.43 1.67e+00 3.59e-01 1.06e+01 angle pdb=" N GLU L 354 " pdb=" CA GLU L 354 " pdb=" CB GLU L 354 " ideal model delta sigma weight residual 110.16 114.87 -4.71 1.48e+00 4.57e-01 1.01e+01 ... (remaining 73397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 30355 16.48 - 32.96: 2682 32.96 - 49.44: 583 49.44 - 65.92: 104 65.92 - 82.40: 44 Dihedral angle restraints: 33768 sinusoidal: 13076 harmonic: 20692 Sorted by residual: dihedral pdb=" CA MET M 233 " pdb=" C MET M 233 " pdb=" N LEU M 234 " pdb=" CA LEU M 234 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA MET C 233 " pdb=" C MET C 233 " pdb=" N LEU C 234 " pdb=" CA LEU C 234 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN B 351 " pdb=" C GLN B 351 " pdb=" N GLN B 352 " pdb=" CA GLN B 352 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 33765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6060 0.031 - 0.062: 1838 0.062 - 0.093: 617 0.093 - 0.124: 399 0.124 - 0.155: 18 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CA GLN B 352 " pdb=" N GLN B 352 " pdb=" C GLN B 352 " pdb=" CB GLN B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA GLN B 351 " pdb=" N GLN B 351 " pdb=" C GLN B 351 " pdb=" CB GLN B 351 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ARG H 362 " pdb=" N ARG H 362 " pdb=" C ARG H 362 " pdb=" CB ARG H 362 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 8929 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 362 " 0.113 9.50e-02 1.11e+02 5.12e-02 2.00e+00 pdb=" NE ARG H 362 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 362 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG H 362 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 362 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 351 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C GLN H 351 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN H 351 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN H 352 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 207 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO E 208 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 208 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 208 " -0.019 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3121 2.73 - 3.27: 57433 3.27 - 3.82: 96350 3.82 - 4.36: 107397 4.36 - 4.90: 189128 Nonbonded interactions: 453429 Sorted by model distance: nonbonded pdb=" O PHE F 195 " pdb=" OG1 THR F 329 " model vdw 2.189 3.040 nonbonded pdb=" O VAL E 263 " pdb=" OG1 THR E 266 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR K 478 " pdb=" OE1 GLU K 483 " model vdw 2.227 3.040 nonbonded pdb=" OD2 ASP N 291 " pdb=" NH1 ARG N 368 " model vdw 2.228 3.120 nonbonded pdb=" O VAL F 263 " pdb=" OG1 THR F 266 " model vdw 2.228 3.040 ... (remaining 453424 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: 0.00 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' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.040 Extract box with map and model: 1.680 Check model and map are aligned: 0.320 Set scattering table: 0.370 Process input model: 99.510 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54362 Z= 0.185 Angle : 0.476 8.456 73402 Z= 0.259 Chirality : 0.039 0.155 8932 Planarity : 0.003 0.051 9618 Dihedral : 13.283 82.402 20496 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4214 sheet: 0.99 (0.15), residues: 1148 loop : -0.19 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 401 PHE 0.015 0.001 PHE F 204 TYR 0.013 0.001 TYR F 203 ARG 0.012 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 4.817 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9559 (tppt) cc_final: 0.9335 (tppt) REVERT: C 389 MET cc_start: 0.8819 (tmm) cc_final: 0.8584 (tmm) REVERT: F 231 ARG cc_start: 0.9365 (mtp85) cc_final: 0.8554 (tpm170) REVERT: F 307 MET cc_start: 0.8222 (pmm) cc_final: 0.8015 (pmm) REVERT: G 307 MET cc_start: 0.8450 (pmm) cc_final: 0.8100 (pmm) REVERT: G 488 MET cc_start: 0.9121 (mmm) cc_final: 0.8700 (mmm) REVERT: H 229 ASN cc_start: 0.9020 (t0) cc_final: 0.8778 (t0) REVERT: H 488 MET cc_start: 0.7964 (mpp) cc_final: 0.7536 (mpt) REVERT: K 389 MET cc_start: 0.8831 (tmm) cc_final: 0.8599 (tmt) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 1.4700 time to fit residues: 652.4790 Evaluate side-chains 297 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 6.9990 chunk 551 optimal weight: 40.0000 chunk 306 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 372 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 570 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 346 optimal weight: 40.0000 chunk 424 optimal weight: 0.7980 chunk 661 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 436 GLN A 505 GLN B 467 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN H 505 GLN ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 GLN J 505 GLN L 319 GLN L 348 GLN M 319 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54362 Z= 0.242 Angle : 0.528 8.414 73402 Z= 0.284 Chirality : 0.041 0.188 8932 Planarity : 0.003 0.034 9618 Dihedral : 3.723 16.526 7728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.60 % Allowed : 5.98 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.10), residues: 7308 helix: 2.43 (0.08), residues: 4228 sheet: 0.85 (0.15), residues: 1064 loop : -0.14 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 401 PHE 0.018 0.001 PHE F 204 TYR 0.012 0.001 TYR F 360 ARG 0.008 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9575 (tppt) cc_final: 0.9355 (tppt) REVERT: C 389 MET cc_start: 0.8913 (tmm) cc_final: 0.8694 (tmm) REVERT: D 167 ASP cc_start: 0.8500 (m-30) cc_final: 0.8293 (m-30) REVERT: D 233 MET cc_start: 0.8941 (pmt) cc_final: 0.8523 (ppp) REVERT: D 389 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7844 (tpp) REVERT: E 231 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8372 (ttp80) REVERT: F 307 MET cc_start: 0.8168 (pmm) cc_final: 0.7942 (pmm) REVERT: G 69 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8342 (mtt) REVERT: G 307 MET cc_start: 0.8544 (pmm) cc_final: 0.8195 (pmm) REVERT: G 488 MET cc_start: 0.8953 (mmm) cc_final: 0.8574 (mmm) REVERT: H 229 ASN cc_start: 0.8997 (t0) cc_final: 0.8783 (OUTLIER) REVERT: H 307 MET cc_start: 0.8812 (ppp) cc_final: 0.8467 (pmm) REVERT: I 16 MET cc_start: 0.7998 (mmp) cc_final: 0.7756 (mtp) REVERT: I 111 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: I 307 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7770 (pp-130) REVERT: I 389 MET cc_start: 0.8827 (tmm) cc_final: 0.8529 (tmm) REVERT: I 520 MET cc_start: 0.8721 (mtp) cc_final: 0.8468 (mtp) REVERT: K 233 MET cc_start: 0.8921 (ppp) cc_final: 0.8680 (ppp) REVERT: K 389 MET cc_start: 0.8866 (tmm) cc_final: 0.8586 (tmt) REVERT: L 193 MET cc_start: 0.8632 (ptm) cc_final: 0.7753 (tmt) REVERT: L 520 MET cc_start: 0.7046 (mtt) cc_final: 0.6673 (mtt) outliers start: 34 outliers final: 8 residues processed: 318 average time/residue: 1.5087 time to fit residues: 601.9433 Evaluate side-chains 304 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 293 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain M residue 354 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 550 optimal weight: 3.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 662 optimal weight: 20.0000 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 0.0060 chunk 656 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 531 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN H 505 GLN I 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 54362 Z= 0.254 Angle : 0.504 9.570 73402 Z= 0.271 Chirality : 0.040 0.167 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.721 17.393 7728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.83 % Allowed : 8.12 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.10), residues: 7308 helix: 2.44 (0.08), residues: 4228 sheet: 0.65 (0.15), residues: 1064 loop : -0.17 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 401 PHE 0.013 0.001 PHE N 44 TYR 0.016 0.001 TYR N 360 ARG 0.004 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 4.769 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: A 160 LYS cc_start: 0.9568 (tppt) cc_final: 0.9327 (tppt) REVERT: A 307 MET cc_start: 0.8418 (pmt) cc_final: 0.7956 (pmm) REVERT: A 389 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7194 (tpt) REVERT: C 389 MET cc_start: 0.8994 (tmm) cc_final: 0.8547 (tmm) REVERT: D 144 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9126 (mp) REVERT: D 167 ASP cc_start: 0.8534 (m-30) cc_final: 0.8316 (m-30) REVERT: D 233 MET cc_start: 0.8887 (pmt) cc_final: 0.8296 (ppp) REVERT: D 389 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7924 (tpp) REVERT: E 231 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8355 (ttp80) REVERT: E 307 MET cc_start: 0.8303 (pmt) cc_final: 0.8044 (pmm) REVERT: F 204 PHE cc_start: 0.8574 (m-80) cc_final: 0.8312 (m-80) REVERT: F 233 MET cc_start: 0.8825 (pmt) cc_final: 0.8053 (ppp) REVERT: G 69 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: G 307 MET cc_start: 0.8591 (pmm) cc_final: 0.8247 (pmm) REVERT: G 488 MET cc_start: 0.8945 (mmm) cc_final: 0.8511 (mmm) REVERT: H 307 MET cc_start: 0.8873 (ppp) cc_final: 0.8544 (pmm) REVERT: I 16 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: I 111 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7980 (mtp) REVERT: I 307 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: K 233 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8793 (ppp) REVERT: K 307 MET cc_start: 0.8262 (tpt) cc_final: 0.7981 (tpp) REVERT: K 389 MET cc_start: 0.8914 (tmm) cc_final: 0.8595 (tmt) REVERT: L 193 MET cc_start: 0.8654 (ptm) cc_final: 0.7868 (tmt) outliers start: 47 outliers final: 14 residues processed: 325 average time/residue: 1.4350 time to fit residues: 586.0427 Evaluate side-chains 312 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 290 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 3.9990 chunk 497 optimal weight: 0.8980 chunk 343 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 444 optimal weight: 9.9990 chunk 664 optimal weight: 8.9990 chunk 703 optimal weight: 6.9990 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 6.9990 chunk 189 optimal weight: 40.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 54362 Z= 0.284 Angle : 0.515 9.813 73402 Z= 0.274 Chirality : 0.041 0.162 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.748 17.961 7728 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.95 % Allowed : 10.22 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4242 sheet: 0.53 (0.15), residues: 1064 loop : -0.13 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 401 PHE 0.015 0.001 PHE L 195 TYR 0.015 0.001 TYR E 360 ARG 0.004 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 5.100 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: A 160 LYS cc_start: 0.9568 (tppt) cc_final: 0.9319 (tppt) REVERT: A 307 MET cc_start: 0.8497 (pmt) cc_final: 0.8147 (pmm) REVERT: A 389 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7243 (tpt) REVERT: B 111 MET cc_start: 0.8400 (mpp) cc_final: 0.8116 (mtp) REVERT: B 351 GLN cc_start: 0.9325 (pp30) cc_final: 0.9034 (pp30) REVERT: B 352 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8716 (mp10) REVERT: B 389 MET cc_start: 0.8862 (tmt) cc_final: 0.8656 (tmt) REVERT: C 233 MET cc_start: 0.8920 (pmt) cc_final: 0.8537 (pmm) REVERT: C 389 MET cc_start: 0.9035 (tmm) cc_final: 0.8626 (tmm) REVERT: D 144 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9109 (mp) REVERT: D 167 ASP cc_start: 0.8522 (m-30) cc_final: 0.8280 (m-30) REVERT: D 233 MET cc_start: 0.8813 (pmt) cc_final: 0.8361 (ppp) REVERT: D 389 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7920 (tpp) REVERT: E 193 MET cc_start: 0.8720 (ptm) cc_final: 0.8232 (pp-130) REVERT: E 231 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8410 (ttp80) REVERT: E 307 MET cc_start: 0.8346 (pmt) cc_final: 0.8085 (pmm) REVERT: F 204 PHE cc_start: 0.8551 (m-80) cc_final: 0.8268 (m-80) REVERT: F 307 MET cc_start: 0.8493 (pmm) cc_final: 0.8258 (pmm) REVERT: G 307 MET cc_start: 0.8622 (pmm) cc_final: 0.8298 (pmm) REVERT: G 397 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8443 (tp30) REVERT: G 488 MET cc_start: 0.8964 (mmm) cc_final: 0.8568 (mmm) REVERT: H 250 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8407 (pp) REVERT: H 307 MET cc_start: 0.8924 (ppp) cc_final: 0.8613 (pmm) REVERT: I 16 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7926 (mtp) REVERT: I 111 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: I 307 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (pp-130) REVERT: I 389 MET cc_start: 0.8856 (tmm) cc_final: 0.8446 (tmm) REVERT: K 233 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8795 (ppp) REVERT: K 307 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8032 (mtm) REVERT: K 389 MET cc_start: 0.8905 (tmm) cc_final: 0.8532 (tmt) REVERT: L 193 MET cc_start: 0.8684 (ptm) cc_final: 0.7872 (tmt) REVERT: L 288 MET cc_start: 0.6317 (ptp) cc_final: 0.6063 (ptm) REVERT: N 250 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8661 (pp) outliers start: 54 outliers final: 15 residues processed: 333 average time/residue: 1.4812 time to fit residues: 619.6434 Evaluate side-chains 323 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 523 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 5.9990 chunk 486 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 631 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54362 Z= 0.295 Angle : 0.526 10.308 73402 Z= 0.278 Chirality : 0.041 0.158 8932 Planarity : 0.003 0.029 9618 Dihedral : 3.770 18.852 7728 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.99 % Allowed : 11.19 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.10), residues: 7308 helix: 2.37 (0.08), residues: 4242 sheet: 0.47 (0.15), residues: 1064 loop : -0.15 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 401 PHE 0.015 0.001 PHE G 44 TYR 0.018 0.001 TYR N 360 ARG 0.003 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 4.895 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: A 160 LYS cc_start: 0.9568 (tppt) cc_final: 0.9316 (tppt) REVERT: A 389 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7235 (tpt) REVERT: B 351 GLN cc_start: 0.9315 (pp30) cc_final: 0.9019 (pp30) REVERT: B 352 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: C 389 MET cc_start: 0.9055 (tmm) cc_final: 0.8567 (tmm) REVERT: D 144 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9085 (mp) REVERT: D 167 ASP cc_start: 0.8538 (m-30) cc_final: 0.8301 (m-30) REVERT: D 233 MET cc_start: 0.8823 (pmt) cc_final: 0.8395 (ppp) REVERT: D 267 MET cc_start: 0.9063 (mmm) cc_final: 0.8587 (mpp) REVERT: D 389 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.7961 (tpp) REVERT: E 231 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8442 (ttp80) REVERT: E 307 MET cc_start: 0.8411 (pmt) cc_final: 0.8138 (pmm) REVERT: E 389 MET cc_start: 0.8496 (tmt) cc_final: 0.8156 (tmt) REVERT: F 204 PHE cc_start: 0.8543 (m-80) cc_final: 0.8235 (m-80) REVERT: F 233 MET cc_start: 0.8768 (pmt) cc_final: 0.8395 (ppp) REVERT: F 307 MET cc_start: 0.8388 (pmm) cc_final: 0.8159 (pmt) REVERT: G 307 MET cc_start: 0.8621 (pmm) cc_final: 0.8289 (pmm) REVERT: G 397 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8463 (tp30) REVERT: G 488 MET cc_start: 0.8977 (mmm) cc_final: 0.8608 (mmm) REVERT: H 250 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (pp) REVERT: H 307 MET cc_start: 0.8988 (ppp) cc_final: 0.8650 (pmm) REVERT: I 16 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7977 (mtp) REVERT: I 111 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: I 307 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7801 (pp-130) REVERT: I 389 MET cc_start: 0.8827 (tmm) cc_final: 0.8354 (tmm) REVERT: J 73 MET cc_start: 0.8653 (mtp) cc_final: 0.8443 (mtm) REVERT: K 111 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: K 233 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8805 (ppp) REVERT: K 389 MET cc_start: 0.8926 (tmm) cc_final: 0.8514 (tmt) REVERT: L 288 MET cc_start: 0.6369 (ptp) cc_final: 0.6144 (ptm) REVERT: M 307 MET cc_start: 0.7967 (tpt) cc_final: 0.7112 (mtp) REVERT: N 250 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (pp) outliers start: 56 outliers final: 21 residues processed: 335 average time/residue: 1.4066 time to fit residues: 593.3231 Evaluate side-chains 327 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 0.7980 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 413 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 704 optimal weight: 40.0000 chunk 584 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54362 Z= 0.225 Angle : 0.511 11.452 73402 Z= 0.271 Chirality : 0.040 0.156 8932 Planarity : 0.003 0.029 9618 Dihedral : 3.745 19.524 7728 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.94 % Allowed : 12.13 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.10), residues: 7308 helix: 2.41 (0.08), residues: 4242 sheet: 0.45 (0.15), residues: 1064 loop : -0.14 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 401 PHE 0.012 0.001 PHE L 195 TYR 0.015 0.001 TYR E 360 ARG 0.002 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 4.951 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: A 160 LYS cc_start: 0.9568 (tppt) cc_final: 0.9299 (tppt) REVERT: A 389 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: B 204 PHE cc_start: 0.8716 (m-80) cc_final: 0.8474 (m-80) REVERT: B 352 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8696 (mp10) REVERT: C 233 MET cc_start: 0.8952 (pmt) cc_final: 0.8559 (pmm) REVERT: C 389 MET cc_start: 0.9056 (tmm) cc_final: 0.8613 (tmm) REVERT: D 144 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9115 (mp) REVERT: D 167 ASP cc_start: 0.8535 (m-30) cc_final: 0.8295 (m-30) REVERT: D 389 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7981 (tpp) REVERT: E 231 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8506 (ttp80) REVERT: E 307 MET cc_start: 0.8505 (pmt) cc_final: 0.8214 (pmm) REVERT: E 389 MET cc_start: 0.8526 (tmt) cc_final: 0.8157 (tmt) REVERT: F 111 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (mtt) REVERT: F 204 PHE cc_start: 0.8534 (m-80) cc_final: 0.8209 (m-80) REVERT: F 233 MET cc_start: 0.8745 (pmt) cc_final: 0.7898 (ppp) REVERT: F 307 MET cc_start: 0.8424 (pmm) cc_final: 0.8173 (pmm) REVERT: G 307 MET cc_start: 0.8639 (pmm) cc_final: 0.8298 (pmm) REVERT: G 397 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8445 (tp30) REVERT: G 488 MET cc_start: 0.8986 (mmm) cc_final: 0.8642 (mmm) REVERT: H 250 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8348 (pp) REVERT: I 16 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7965 (mtp) REVERT: I 307 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (pp-130) REVERT: I 389 MET cc_start: 0.8842 (tmm) cc_final: 0.8362 (tmm) REVERT: K 111 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8159 (mtt) REVERT: K 233 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8751 (ppp) REVERT: K 389 MET cc_start: 0.8961 (tmm) cc_final: 0.8554 (tmt) REVERT: L 193 MET cc_start: 0.8667 (ptm) cc_final: 0.7865 (tmt) REVERT: L 288 MET cc_start: 0.6456 (ptp) cc_final: 0.6250 (ptm) REVERT: M 307 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7744 (tpp) REVERT: N 250 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8658 (pp) outliers start: 53 outliers final: 26 residues processed: 336 average time/residue: 1.4488 time to fit residues: 612.5410 Evaluate side-chains 331 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 9.9990 chunk 79 optimal weight: 40.0000 chunk 401 optimal weight: 20.0000 chunk 514 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 592 optimal weight: 0.1980 chunk 393 optimal weight: 9.9990 chunk 701 optimal weight: 40.0000 chunk 439 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 323 optimal weight: 0.8980 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 453 GLN ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54362 Z= 0.282 Angle : 0.538 12.620 73402 Z= 0.284 Chirality : 0.041 0.163 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.766 19.383 7728 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.01 % Allowed : 12.82 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.10), residues: 7308 helix: 2.36 (0.08), residues: 4242 sheet: 0.42 (0.15), residues: 1064 loop : -0.16 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.018 0.001 PHE G 44 TYR 0.020 0.001 TYR N 360 ARG 0.002 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 4.973 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: A 160 LYS cc_start: 0.9570 (tppt) cc_final: 0.9297 (tppt) REVERT: A 389 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7253 (tpt) REVERT: B 352 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8771 (mp10) REVERT: C 233 MET cc_start: 0.8901 (pmt) cc_final: 0.8501 (pmm) REVERT: C 389 MET cc_start: 0.9075 (tmm) cc_final: 0.8590 (tmm) REVERT: D 144 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9124 (mp) REVERT: D 167 ASP cc_start: 0.8558 (m-30) cc_final: 0.8318 (m-30) REVERT: D 233 MET cc_start: 0.8868 (pmt) cc_final: 0.8413 (ppp) REVERT: D 267 MET cc_start: 0.8688 (mmp) cc_final: 0.8402 (mpp) REVERT: D 389 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7987 (tpp) REVERT: E 193 MET cc_start: 0.8764 (ptm) cc_final: 0.8053 (pp-130) REVERT: E 231 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8513 (ttp80) REVERT: E 307 MET cc_start: 0.8537 (pmt) cc_final: 0.8251 (pmm) REVERT: F 111 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: F 233 MET cc_start: 0.8734 (pmt) cc_final: 0.7908 (ppp) REVERT: F 307 MET cc_start: 0.8364 (pmm) cc_final: 0.8084 (pmm) REVERT: G 307 MET cc_start: 0.8642 (pmm) cc_final: 0.8300 (pmm) REVERT: G 397 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8459 (tp30) REVERT: G 488 MET cc_start: 0.8978 (mmm) cc_final: 0.8640 (mmm) REVERT: H 250 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8366 (pp) REVERT: H 307 MET cc_start: 0.8604 (pmt) cc_final: 0.8360 (pmm) REVERT: I 16 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: I 307 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (pp-130) REVERT: I 389 MET cc_start: 0.8858 (tmm) cc_final: 0.8360 (tmm) REVERT: J 389 MET cc_start: 0.8802 (tmt) cc_final: 0.8034 (tmm) REVERT: K 111 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: K 233 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8804 (ppp) REVERT: K 389 MET cc_start: 0.8952 (tmm) cc_final: 0.8546 (tmt) REVERT: L 193 MET cc_start: 0.8673 (ptm) cc_final: 0.7901 (tmt) REVERT: M 288 MET cc_start: 0.7442 (mtm) cc_final: 0.7024 (pp-130) REVERT: M 307 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7161 (mtp) REVERT: N 250 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8647 (pp) outliers start: 57 outliers final: 28 residues processed: 337 average time/residue: 1.4711 time to fit residues: 623.7365 Evaluate side-chains 332 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain N residue 69 MET Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 30.0000 chunk 280 optimal weight: 8.9990 chunk 419 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 346 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 551 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 54362 Z= 0.298 Angle : 0.550 13.250 73402 Z= 0.290 Chirality : 0.041 0.171 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.778 19.237 7728 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.99 % Allowed : 13.22 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 7308 helix: 2.34 (0.08), residues: 4242 sheet: 0.40 (0.15), residues: 1064 loop : -0.17 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.011 0.001 PHE L 195 TYR 0.016 0.001 TYR E 360 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 4.848 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 160 LYS cc_start: 0.9570 (tppt) cc_final: 0.9295 (tppt) REVERT: A 389 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7257 (tpt) REVERT: C 233 MET cc_start: 0.8873 (pmt) cc_final: 0.8480 (pmm) REVERT: C 389 MET cc_start: 0.9084 (tmm) cc_final: 0.8594 (tmm) REVERT: D 144 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9119 (mp) REVERT: D 167 ASP cc_start: 0.8571 (m-30) cc_final: 0.8332 (m-30) REVERT: D 233 MET cc_start: 0.8866 (pmt) cc_final: 0.8452 (ppp) REVERT: D 389 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8012 (tpp) REVERT: E 193 MET cc_start: 0.8747 (ptm) cc_final: 0.8018 (pp-130) REVERT: E 231 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8508 (ttp80) REVERT: E 307 MET cc_start: 0.8580 (pmt) cc_final: 0.8289 (pmm) REVERT: E 389 MET cc_start: 0.8502 (tmt) cc_final: 0.8245 (tmt) REVERT: F 111 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7911 (mtt) REVERT: F 307 MET cc_start: 0.8355 (pmm) cc_final: 0.8070 (pmm) REVERT: G 69 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: G 307 MET cc_start: 0.8641 (pmm) cc_final: 0.8299 (pmm) REVERT: G 397 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8471 (tp30) REVERT: G 488 MET cc_start: 0.8972 (mmm) cc_final: 0.8458 (mmm) REVERT: H 250 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8374 (pp) REVERT: H 307 MET cc_start: 0.8630 (pmt) cc_final: 0.8347 (pmm) REVERT: I 16 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: I 307 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7830 (pp-130) REVERT: I 389 MET cc_start: 0.8861 (tmm) cc_final: 0.8399 (tmm) REVERT: K 111 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: K 233 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8804 (ppp) REVERT: K 389 MET cc_start: 0.8953 (tmm) cc_final: 0.8532 (tmm) REVERT: L 193 MET cc_start: 0.8676 (ptm) cc_final: 0.7882 (tmt) REVERT: M 307 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7139 (mtp) REVERT: N 250 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8649 (pp) outliers start: 56 outliers final: 31 residues processed: 331 average time/residue: 1.4388 time to fit residues: 600.5361 Evaluate side-chains 335 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain N residue 69 MET Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 9.9990 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.7980 chunk 653 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 513 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 590 optimal weight: 20.0000 chunk 618 optimal weight: 0.9990 chunk 651 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN J 153 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54362 Z= 0.151 Angle : 0.529 12.706 73402 Z= 0.279 Chirality : 0.040 0.194 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.723 19.596 7728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.88 % Allowed : 13.56 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.10), residues: 7308 helix: 2.43 (0.08), residues: 4256 sheet: 0.46 (0.15), residues: 1064 loop : -0.18 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 401 PHE 0.021 0.001 PHE G 44 TYR 0.020 0.001 TYR N 360 ARG 0.003 0.000 ARG L 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 4.901 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: A 160 LYS cc_start: 0.9563 (tppt) cc_final: 0.9286 (tppt) REVERT: A 389 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7333 (tpt) REVERT: B 204 PHE cc_start: 0.8758 (m-80) cc_final: 0.8547 (m-80) REVERT: C 166 MET cc_start: 0.9118 (tpp) cc_final: 0.8577 (mtp) REVERT: C 233 MET cc_start: 0.8834 (pmt) cc_final: 0.8458 (pmm) REVERT: C 389 MET cc_start: 0.9083 (tmm) cc_final: 0.8638 (tmm) REVERT: D 167 ASP cc_start: 0.8558 (m-30) cc_final: 0.8353 (m-30) REVERT: D 233 MET cc_start: 0.8847 (pmt) cc_final: 0.8373 (ppp) REVERT: D 389 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8066 (tpp) REVERT: E 193 MET cc_start: 0.8753 (ptm) cc_final: 0.8114 (pp-130) REVERT: E 231 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8489 (ttp80) REVERT: E 307 MET cc_start: 0.8570 (pmt) cc_final: 0.8248 (pmm) REVERT: F 307 MET cc_start: 0.8333 (pmm) cc_final: 0.8040 (pmm) REVERT: F 389 MET cc_start: 0.7613 (tmt) cc_final: 0.7141 (tpp) REVERT: G 397 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8408 (tp30) REVERT: G 488 MET cc_start: 0.8987 (mmm) cc_final: 0.8525 (mmm) REVERT: H 193 MET cc_start: 0.8904 (ptm) cc_final: 0.8525 (ppp) REVERT: H 250 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8155 (pp) REVERT: H 307 MET cc_start: 0.8591 (pmt) cc_final: 0.8270 (pmm) REVERT: H 351 GLN cc_start: 0.9492 (pp30) cc_final: 0.9251 (pp30) REVERT: H 354 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9169 (pp20) REVERT: I 16 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7873 (mtp) REVERT: I 389 MET cc_start: 0.8851 (tmm) cc_final: 0.8381 (tmm) REVERT: J 389 MET cc_start: 0.8761 (tmt) cc_final: 0.7974 (tmm) REVERT: K 111 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8094 (mtt) REVERT: K 233 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8741 (ppp) REVERT: K 389 MET cc_start: 0.8996 (tmm) cc_final: 0.8582 (tmm) REVERT: L 193 MET cc_start: 0.8668 (ptm) cc_final: 0.7927 (tmt) REVERT: M 288 MET cc_start: 0.7367 (mtm) cc_final: 0.6977 (pp-130) REVERT: M 307 MET cc_start: 0.7972 (tpt) cc_final: 0.7184 (mtm) REVERT: N 250 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8640 (pp) outliers start: 50 outliers final: 22 residues processed: 340 average time/residue: 1.4976 time to fit residues: 638.1136 Evaluate side-chains 326 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 5.9990 chunk 691 optimal weight: 20.0000 chunk 422 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 480 optimal weight: 7.9990 chunk 725 optimal weight: 0.1980 chunk 667 optimal weight: 7.9990 chunk 577 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 505 GLN ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 GLN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54362 Z= 0.239 Angle : 0.555 13.333 73402 Z= 0.290 Chirality : 0.041 0.271 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.748 19.401 7728 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.78 % Allowed : 13.97 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.10), residues: 7308 helix: 2.38 (0.08), residues: 4256 sheet: 0.46 (0.15), residues: 1064 loop : -0.20 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.020 0.001 PHE G 44 TYR 0.016 0.001 TYR E 360 ARG 0.002 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9568 (tppt) cc_final: 0.9292 (tppt) REVERT: A 389 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7258 (tpt) REVERT: C 166 MET cc_start: 0.9123 (tpp) cc_final: 0.8552 (mtp) REVERT: C 233 MET cc_start: 0.8842 (pmt) cc_final: 0.8479 (pmm) REVERT: C 389 MET cc_start: 0.9095 (tmm) cc_final: 0.8660 (tmm) REVERT: C 491 MET cc_start: 0.9126 (mtt) cc_final: 0.8917 (mtt) REVERT: D 167 ASP cc_start: 0.8562 (m-30) cc_final: 0.8324 (m-30) REVERT: D 233 MET cc_start: 0.8848 (pmt) cc_final: 0.8422 (ppp) REVERT: D 389 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8021 (tpp) REVERT: E 193 MET cc_start: 0.8763 (ptm) cc_final: 0.8056 (pp-130) REVERT: E 231 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8494 (ttp80) REVERT: E 307 MET cc_start: 0.8588 (pmt) cc_final: 0.8285 (pmm) REVERT: F 307 MET cc_start: 0.8196 (pmm) cc_final: 0.7890 (pmm) REVERT: G 59 GLU cc_start: 0.8280 (tp30) cc_final: 0.7843 (tp30) REVERT: G 164 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: G 397 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8433 (tp30) REVERT: G 488 MET cc_start: 0.8922 (mmm) cc_final: 0.8557 (mmm) REVERT: H 193 MET cc_start: 0.8911 (ptm) cc_final: 0.8502 (ppp) REVERT: H 250 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8191 (pp) REVERT: H 307 MET cc_start: 0.8594 (pmt) cc_final: 0.8208 (pmm) REVERT: H 351 GLN cc_start: 0.9488 (pp30) cc_final: 0.9257 (pp30) REVERT: H 354 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.9164 (pp20) REVERT: I 16 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7792 (mtp) REVERT: I 389 MET cc_start: 0.8862 (tmm) cc_final: 0.8316 (tmm) REVERT: J 389 MET cc_start: 0.8779 (tmt) cc_final: 0.8006 (tmm) REVERT: K 111 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: K 233 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (ppp) REVERT: K 389 MET cc_start: 0.8963 (tmm) cc_final: 0.8560 (tmt) REVERT: L 193 MET cc_start: 0.8694 (ptm) cc_final: 0.7914 (tmt) REVERT: M 288 MET cc_start: 0.7420 (mtm) cc_final: 0.6981 (pp-130) REVERT: M 307 MET cc_start: 0.7996 (tpt) cc_final: 0.7192 (mtm) REVERT: N 250 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8645 (pp) outliers start: 44 outliers final: 24 residues processed: 325 average time/residue: 1.5283 time to fit residues: 621.9781 Evaluate side-chains 325 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 233 MET Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 6.9990 chunk 615 optimal weight: 0.9990 chunk 176 optimal weight: 20.0000 chunk 532 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 0.4980 chunk 578 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 GLN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055957 restraints weight = 159145.797| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.28 r_work: 0.2954 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54362 Z= 0.170 Angle : 0.541 13.059 73402 Z= 0.283 Chirality : 0.040 0.266 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.728 19.440 7728 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.67 % Allowed : 14.13 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4256 sheet: 0.48 (0.16), residues: 1064 loop : -0.19 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.020 0.001 PHE N 44 TYR 0.020 0.001 TYR N 360 ARG 0.002 0.000 ARG N 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11438.45 seconds wall clock time: 201 minutes 59.14 seconds (12119.14 seconds total)