Starting phenix.real_space_refine on Wed Sep 25 05:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/09_2024/7xok_33350.cif" } resolution = 2.7 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 15 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 23.04, per 1000 atoms: 0.43 Number of scatterers: 53970 At special positions: 0 Unit cell: (155.73, 160.08, 155.73, 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: 10.62 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: 264 helices and 84 sheets defined 59.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.144A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.501A 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 Processing helix chain 'A' and resid 229 through 244 removed outlier: 4.374A pdb=" N MET A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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: 3.710A 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: 4.039A 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: 4.128A 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 109 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: 3.629A 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: 4.324A 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 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: 3.954A 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 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.039A 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: 3.602A 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 308 through 312 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: 3.845A 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 removed outlier: 3.500A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) 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: 4.102A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.510A 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: 3.558A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.521A pdb=" N MET D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix 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: 3.913A 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 removed outlier: 3.545A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.191A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 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: 3.591A 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: 4.362A 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: 4.026A 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: 4.232A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.519A 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: 3.558A 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: 3.966A 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: 4.103A 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 109 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: 3.700A 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: 4.236A 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: 3.828A 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: 4.131A 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: 3.627A 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 244 removed outlier: 4.359A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix 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 Processing helix chain 'H' and resid 358 through 375 removed outlier: 4.095A 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: 3.826A 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: 4.093A 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 110 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: 3.572A 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 244 removed outlier: 4.418A pdb=" N MET I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.840A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) removed outlier: 3.793A 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: 4.236A 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: 3.851A 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 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.037A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 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: 3.611A 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: 4.234A 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: 3.866A 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: 4.139A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 59 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: 3.580A 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: 4.296A 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: 3.890A 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 removed outlier: 3.513A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.141A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 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: 3.569A 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: 4.427A 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: 3.620A 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: 3.954A 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: 4.126A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 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: 3.534A 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 313 through 317 Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.752A pdb=" N ILE M 342 " --> pdb=" O GLU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 removed outlier: 4.125A 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: 3.957A 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 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.062A 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: 3.642A 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 244 removed outlier: 4.396A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix 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: 3.590A 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: 3.897A 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 removed outlier: 3.505A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A) 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: 6.492A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.166A 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: 6.345A pdb=" N ASN A 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 4.155A 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: 6.203A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.936A 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: 8.432A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.919A 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: 3.508A 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: 7.012A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.479A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.844A 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: 6.169A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.964A 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=AB2, first strand: chain 'B' and resid 213 through 216 removed outlier: 8.344A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (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: 6.846A pdb=" N ASN C 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL D 521 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.431A 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: 6.531A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.605A 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: 6.201A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 213 through 216 removed outlier: 8.174A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (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: 3.501A 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: 6.526A pdb=" N ASN D 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 4.184A 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 193 through 195 removed outlier: 6.328A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.328A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 251 " --> 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: 3.610A 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: 6.919A pdb=" N ASN E 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL F 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.521A 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: 6.271A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.422A 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: 6.271A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.508A 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: 6.536A pdb=" N ASN F 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS G 519 " --> pdb=" O ASN F 37 " (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: 3.575A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.385A 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: 3.575A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.003A 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: 3.607A 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 removed outlier: 6.557A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.200A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.363A 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: 6.200A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 3.667A 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: 3.508A 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: 6.396A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 4.096A 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: 6.388A pdb=" N ASN H 37 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS I 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS I 7 " --> pdb=" O MET I 520 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.482A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.191A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.045A 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: 8.507A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.092A 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: 3.539A 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: 6.982A pdb=" N ASN I 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL J 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL I 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.631A 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: 6.344A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.191A 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: 8.458A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.938A 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 478 Processing sheet with id=AG2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.977A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.469A 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 193 through 195 removed outlier: 6.264A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.508A 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: 8.405A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.024A 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 removed outlier: 3.510A pdb=" N GLU J 484 " --> pdb=" O ASN J 479 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 48 through 50 removed outlier: 6.490A pdb=" N ASN K 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS L 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS L 7 " --> pdb=" O MET L 520 " (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: 6.226A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.592A 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: 8.417A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.012A 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: 3.571A 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: 6.886A pdb=" N ASN L 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL M 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL L 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.505A 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 193 through 195 removed outlier: 6.193A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.193A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.002A 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 Processing sheet with id=AI2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.871A pdb=" N ASN M 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL N 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.600A 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: 6.584A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.472A 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 removed outlier: 6.181A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.181A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA M 251 " --> pdb=" O VAL M 276 " (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: 3.610A 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 Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.252A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 213 through 216 removed outlier: 8.346A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (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 3822 hydrogen bonds defined for protein. 11004 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: 23.78 Time building geometry restraints manager: 12.55 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: 18690 1.34 - 1.46: 4397 1.46 - 1.57: 30757 1.57 - 1.69: 0 1.69 - 1.81: 518 Bond restraints: 54362 Sorted by residual: bond pdb=" CB MET G 520 " pdb=" CG MET G 520 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CB MET E 520 " pdb=" CG MET E 520 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.74e+00 bond pdb=" CB MET C 520 " pdb=" CG MET C 520 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CA MET E 520 " pdb=" CB MET E 520 " ideal model delta sigma weight residual 1.535 1.505 0.031 2.09e-02 2.29e+03 2.15e+00 bond pdb=" SD MET B 520 " pdb=" CE MET B 520 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 54357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 72772 2.13 - 4.26: 550 4.26 - 6.39: 63 6.39 - 8.53: 14 8.53 - 10.66: 3 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 111.30 121.96 -10.66 2.30e+00 1.89e-01 2.15e+01 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" CB GLU D 164 " ideal model delta sigma weight residual 110.28 116.12 -5.84 1.55e+00 4.16e-01 1.42e+01 angle pdb=" N GLU M 354 " pdb=" CA GLU M 354 " pdb=" CB GLU M 354 " ideal model delta sigma weight residual 110.28 116.10 -5.82 1.55e+00 4.16e-01 1.41e+01 angle pdb=" N GLU H 164 " pdb=" CA GLU H 164 " pdb=" CB GLU H 164 " ideal model delta sigma weight residual 110.16 115.59 -5.43 1.48e+00 4.57e-01 1.34e+01 angle pdb=" N GLN N 352 " pdb=" CA GLN N 352 " pdb=" CB GLN N 352 " ideal model delta sigma weight residual 110.16 115.27 -5.11 1.48e+00 4.57e-01 1.19e+01 ... (remaining 73397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 30381 16.35 - 32.70: 2689 32.70 - 49.04: 546 49.04 - 65.39: 109 65.39 - 81.74: 43 Dihedral angle restraints: 33768 sinusoidal: 13076 harmonic: 20692 Sorted by residual: 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 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 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 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA MET F 233 " pdb=" C MET F 233 " pdb=" N LEU F 234 " pdb=" CA LEU F 234 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 33765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 6527 0.037 - 0.074: 1672 0.074 - 0.111: 637 0.111 - 0.148: 93 0.148 - 0.185: 3 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CA ARG H 350 " pdb=" N ARG H 350 " pdb=" C ARG H 350 " pdb=" CB ARG H 350 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA MET F 447 " pdb=" N MET F 447 " pdb=" C MET F 447 " pdb=" CB MET F 447 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA GLU M 354 " pdb=" N GLU M 354 " pdb=" C GLU M 354 " pdb=" CB GLU M 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 8929 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 362 " 0.162 9.50e-02 1.11e+02 7.31e-02 3.93e+00 pdb=" NE ARG H 362 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 362 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 362 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 362 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 351 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C GLN H 351 " -0.027 2.00e-02 2.50e+03 pdb=" O GLN H 351 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN H 352 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 350 " 0.116 9.50e-02 1.11e+02 5.26e-02 2.31e+00 pdb=" NE ARG H 350 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 350 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 350 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 350 " -0.000 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1381 2.71 - 3.26: 57207 3.26 - 3.80: 94154 3.80 - 4.35: 111710 4.35 - 4.90: 191924 Nonbonded interactions: 456376 Sorted by model distance: nonbonded pdb=" OD2 ASP N 291 " pdb=" NH1 ARG N 368 " model vdw 2.160 3.120 nonbonded pdb=" OG SER A 358 " pdb=" OD2 ASP A 361 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP A 291 " pdb=" NH1 ARG A 368 " model vdw 2.203 3.120 nonbonded pdb=" OD2 ASP F 291 " pdb=" NH2 ARG F 368 " model vdw 2.215 3.120 nonbonded pdb=" OG SER G 463 " pdb=" OG SER M 463 " model vdw 2.215 3.040 ... (remaining 456371 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.690 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 98.570 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 0.058 54362 Z= 0.227 Angle : 0.496 10.656 73402 Z= 0.271 Chirality : 0.039 0.185 8932 Planarity : 0.003 0.073 9618 Dihedral : 13.145 81.741 20496 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.10), residues: 7308 helix: 2.32 (0.08), residues: 4242 sheet: 1.06 (0.15), residues: 1148 loop : -0.15 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.008 0.001 PHE G 204 TYR 0.013 0.001 TYR G 360 ARG 0.014 0.000 ARG H 362 *********************** 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 384 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.770 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.8079 (mmm) cc_final: 0.7799 (mmm) REVERT: C 389 MET cc_start: 0.8905 (tmm) cc_final: 0.8516 (tmm) REVERT: F 59 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8468 (mm-30) REVERT: F 114 MET cc_start: 0.8519 (mmm) cc_final: 0.8282 (mmm) REVERT: H 193 MET cc_start: 0.8479 (ttm) cc_final: 0.8159 (ttm) REVERT: I 307 MET cc_start: 0.8613 (pmm) cc_final: 0.8392 (pmm) REVERT: K 44 PHE cc_start: 0.8091 (m-80) cc_final: 0.7870 (m-10) REVERT: L 138 CYS cc_start: 0.7909 (t) cc_final: 0.7693 (t) outliers start: 0 outliers final: 1 residues processed: 384 average time/residue: 1.4989 time to fit residues: 716.3259 Evaluate side-chains 306 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 473 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 9.9990 chunk 551 optimal weight: 40.0000 chunk 306 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 294 optimal weight: 30.0000 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** 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 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0824 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= 0.256 Angle : 0.540 7.996 73402 Z= 0.290 Chirality : 0.041 0.182 8932 Planarity : 0.003 0.046 9618 Dihedral : 4.002 109.358 7730 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.85 % Allowed : 5.71 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.08), residues: 4242 sheet: 0.82 (0.15), residues: 1064 loop : -0.10 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 401 PHE 0.016 0.001 PHE F 204 TYR 0.014 0.001 TYR D 360 ARG 0.008 0.000 ARG G 58 *********************** 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 390 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 342 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8118 (mmm) cc_final: 0.7790 (mmm) REVERT: A 193 MET cc_start: 0.8664 (ptp) cc_final: 0.8302 (ptt) REVERT: A 255 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 267 MET cc_start: 0.8349 (mmm) cc_final: 0.7865 (mtp) REVERT: B 389 MET cc_start: 0.8662 (tmm) cc_final: 0.7773 (tmm) REVERT: C 389 MET cc_start: 0.8989 (tmm) cc_final: 0.8594 (tmm) REVERT: D 111 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8247 (mpm) REVERT: D 144 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9132 (mp) REVERT: D 389 MET cc_start: 0.8791 (tmm) cc_final: 0.8446 (tmt) REVERT: E 16 MET cc_start: 0.8665 (mtm) cc_final: 0.8201 (mtt) REVERT: F 59 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8460 (mm-30) REVERT: F 114 MET cc_start: 0.8564 (mmm) cc_final: 0.8308 (mmm) REVERT: F 204 PHE cc_start: 0.8161 (m-80) cc_final: 0.7926 (m-80) REVERT: G 307 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8352 (pmt) REVERT: G 397 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8540 (mm-30) REVERT: H 193 MET cc_start: 0.8646 (ttm) cc_final: 0.8303 (ttm) REVERT: H 362 ARG cc_start: 0.9088 (pmt170) cc_final: 0.8787 (ptp90) REVERT: H 491 MET cc_start: 0.8964 (mtm) cc_final: 0.8724 (mtp) REVERT: I 307 MET cc_start: 0.8683 (pmm) cc_final: 0.8408 (pmm) REVERT: I 389 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (tmt) REVERT: J 233 MET cc_start: 0.8784 (pmm) cc_final: 0.8553 (pmm) REVERT: K 44 PHE cc_start: 0.8045 (m-80) cc_final: 0.7834 (m-10) REVERT: K 111 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: L 138 CYS cc_start: 0.8018 (t) cc_final: 0.7750 (t) REVERT: M 233 MET cc_start: 0.8531 (pmt) cc_final: 0.8308 (pmm) REVERT: M 307 MET cc_start: 0.8444 (tpt) cc_final: 0.8219 (tpt) REVERT: N 389 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8247 (tmt) outliers start: 48 outliers final: 7 residues processed: 351 average time/residue: 1.5007 time to fit residues: 656.0975 Evaluate side-chains 323 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 310 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 389 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 550 optimal weight: 7.9990 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 662 optimal weight: 20.0000 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 531 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN F 467 ASN G 319 GLN ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 467 ASN L 229 ASN L 319 GLN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1040 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= 0.323 Angle : 0.540 7.360 73402 Z= 0.288 Chirality : 0.041 0.177 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.837 18.491 7728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.04 % Allowed : 8.40 % Favored : 90.56 % 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: 2.05 (0.10), residues: 7308 helix: 2.28 (0.08), residues: 4228 sheet: 0.60 (0.15), residues: 1064 loop : -0.18 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.013 0.001 PHE B 204 TYR 0.012 0.001 TYR F 199 ARG 0.008 0.000 ARG N 362 *********************** 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 384 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 325 time to evaluate : 4.788 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: A 114 MET cc_start: 0.8111 (mmm) cc_final: 0.7783 (mmm) REVERT: A 193 MET cc_start: 0.8643 (ptp) cc_final: 0.8294 (ptt) REVERT: A 352 GLN cc_start: 0.9315 (mm110) cc_final: 0.9109 (mm110) REVERT: B 389 MET cc_start: 0.8662 (tmm) cc_final: 0.7807 (tmm) REVERT: C 166 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: C 389 MET cc_start: 0.9018 (tmm) cc_final: 0.8618 (tmm) REVERT: D 144 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9138 (mp) REVERT: D 221 LEU cc_start: 0.9417 (tp) cc_final: 0.9164 (tm) REVERT: E 16 MET cc_start: 0.8567 (mtm) cc_final: 0.8285 (mtt) REVERT: E 111 MET cc_start: 0.8772 (mpp) cc_final: 0.8371 (mpt) REVERT: F 59 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8494 (mm-30) REVERT: F 114 MET cc_start: 0.8586 (mmm) cc_final: 0.8332 (mmm) REVERT: F 204 PHE cc_start: 0.8172 (m-80) cc_final: 0.7874 (m-80) REVERT: G 307 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8412 (pmt) REVERT: G 389 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6333 (tmt) REVERT: G 397 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8526 (mm-30) REVERT: H 193 MET cc_start: 0.8601 (ttm) cc_final: 0.8262 (ttm) REVERT: I 307 MET cc_start: 0.8667 (pmm) cc_final: 0.8411 (pmm) REVERT: I 389 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8563 (tmt) REVERT: I 520 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8372 (mtt) REVERT: J 233 MET cc_start: 0.8763 (pmm) cc_final: 0.8477 (pmm) REVERT: J 389 MET cc_start: 0.8833 (tmt) cc_final: 0.8530 (tmt) REVERT: K 44 PHE cc_start: 0.8062 (m-80) cc_final: 0.7851 (m-10) REVERT: L 138 CYS cc_start: 0.8106 (t) cc_final: 0.7800 (t) REVERT: L 146 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.9167 (tm-30) REVERT: L 366 GLN cc_start: 0.9540 (mm110) cc_final: 0.9270 (mm110) REVERT: N 233 MET cc_start: 0.8507 (ppp) cc_final: 0.8257 (ppp) outliers start: 59 outliers final: 14 residues processed: 345 average time/residue: 1.4902 time to fit residues: 640.1114 Evaluate side-chains 329 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 308 time to evaluate : 5.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain N residue 16 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 50.0000 chunk 497 optimal weight: 9.9990 chunk 343 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 444 optimal weight: 20.0000 chunk 664 optimal weight: 5.9990 chunk 703 optimal weight: 6.9990 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 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** I 351 GLN ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** 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: 0.8353 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 54362 Z= 0.319 Angle : 0.537 8.338 73402 Z= 0.286 Chirality : 0.041 0.157 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.854 17.029 7728 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.01 % Allowed : 10.18 % Favored : 88.81 % 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: 2.00 (0.10), residues: 7308 helix: 2.27 (0.08), residues: 4228 sheet: 0.50 (0.15), residues: 1064 loop : -0.20 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.015 0.001 PHE B 204 TYR 0.009 0.001 TYR K 199 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 384 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 327 time to evaluate : 4.724 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 111 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: A 193 MET cc_start: 0.8642 (ptp) cc_final: 0.8353 (ptt) REVERT: A 352 GLN cc_start: 0.9310 (mm110) cc_final: 0.9079 (mm110) REVERT: B 16 MET cc_start: 0.8633 (mmm) cc_final: 0.8358 (mtp) REVERT: B 267 MET cc_start: 0.8434 (mmm) cc_final: 0.7862 (ptm) REVERT: B 389 MET cc_start: 0.8673 (tmm) cc_final: 0.7813 (tmm) REVERT: C 166 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8050 (mtt) REVERT: C 389 MET cc_start: 0.9037 (tmm) cc_final: 0.8634 (tmm) REVERT: D 111 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8291 (mpm) REVERT: D 144 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9125 (mp) REVERT: D 221 LEU cc_start: 0.9475 (tp) cc_final: 0.9244 (tm) REVERT: D 389 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8482 (tmt) REVERT: F 59 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8508 (mm-30) REVERT: F 114 MET cc_start: 0.8586 (mmm) cc_final: 0.8312 (mmm) REVERT: F 204 PHE cc_start: 0.8243 (m-80) cc_final: 0.7914 (m-80) REVERT: F 233 MET cc_start: 0.8365 (pmt) cc_final: 0.7875 (ppp) REVERT: G 389 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6306 (tmt) REVERT: G 397 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8514 (mm-30) REVERT: H 193 MET cc_start: 0.8590 (ttm) cc_final: 0.8281 (ttm) REVERT: I 166 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: I 307 MET cc_start: 0.8672 (pmm) cc_final: 0.8444 (pmm) REVERT: I 389 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8451 (tmt) REVERT: I 520 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: J 233 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (pmm) REVERT: J 250 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8207 (pp) REVERT: K 44 PHE cc_start: 0.8064 (m-80) cc_final: 0.7840 (m-10) REVERT: L 138 CYS cc_start: 0.8127 (t) cc_final: 0.7807 (t) REVERT: L 146 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.9197 (tm-30) REVERT: L 307 MET cc_start: 0.8855 (pmm) cc_final: 0.8593 (pmm) REVERT: L 366 GLN cc_start: 0.9541 (mm110) cc_final: 0.9268 (mm110) REVERT: N 233 MET cc_start: 0.8503 (ppp) cc_final: 0.8262 (ppp) REVERT: N 389 MET cc_start: 0.8456 (tmt) cc_final: 0.8202 (tmt) outliers start: 57 outliers final: 16 residues processed: 351 average time/residue: 1.5560 time to fit residues: 684.9205 Evaluate side-chains 336 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 308 time to evaluate : 4.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 354 GLU Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 354 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 6.9990 chunk 399 optimal weight: 20.0000 chunk 10 optimal weight: 0.3980 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 600 optimal weight: 6.9990 chunk 486 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 631 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 GLN ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 54362 Z= 0.251 Angle : 0.519 8.808 73402 Z= 0.276 Chirality : 0.040 0.157 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.830 18.312 7728 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.03 % Allowed : 11.30 % Favored : 87.68 % 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: 2.03 (0.10), residues: 7308 helix: 2.31 (0.08), residues: 4228 sheet: 0.45 (0.15), residues: 1064 loop : -0.20 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.015 0.001 PHE B 204 TYR 0.009 0.001 TYR K 199 ARG 0.006 0.000 ARG H 362 *********************** 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 387 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 329 time to evaluate : 4.760 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 193 MET cc_start: 0.8632 (ptp) cc_final: 0.8345 (ptt) REVERT: A 352 GLN cc_start: 0.9299 (mm110) cc_final: 0.9089 (mm110) REVERT: B 16 MET cc_start: 0.8573 (mmm) cc_final: 0.8353 (mtm) REVERT: B 250 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8235 (pp) REVERT: B 254 VAL cc_start: 0.9391 (t) cc_final: 0.9189 (p) REVERT: B 520 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7568 (mtt) REVERT: C 389 MET cc_start: 0.9049 (tmm) cc_final: 0.8653 (tmm) REVERT: D 111 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8273 (mpm) REVERT: D 144 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9127 (mp) REVERT: D 164 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: D 389 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8454 (tmt) REVERT: E 193 MET cc_start: 0.8245 (ppp) cc_final: 0.8030 (tmm) REVERT: F 59 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8496 (mm-30) REVERT: F 114 MET cc_start: 0.8582 (mmm) cc_final: 0.8320 (mmm) REVERT: F 204 PHE cc_start: 0.8224 (m-80) cc_final: 0.7875 (m-80) REVERT: F 233 MET cc_start: 0.8446 (pmt) cc_final: 0.7852 (ppp) REVERT: F 520 MET cc_start: 0.8663 (mtp) cc_final: 0.8452 (mtp) REVERT: G 389 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6330 (tmt) REVERT: G 397 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8564 (mm-30) REVERT: H 193 MET cc_start: 0.8569 (ttm) cc_final: 0.8280 (ttm) REVERT: I 389 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8470 (tmt) REVERT: I 520 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8477 (mtt) REVERT: J 233 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8524 (pmm) REVERT: J 250 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8246 (pp) REVERT: J 389 MET cc_start: 0.8847 (tmt) cc_final: 0.8589 (tmt) REVERT: J 488 MET cc_start: 0.9209 (mmm) cc_final: 0.8890 (mmm) REVERT: K 44 PHE cc_start: 0.8062 (m-80) cc_final: 0.7833 (m-10) REVERT: K 307 MET cc_start: 0.8881 (mpm) cc_final: 0.8611 (mpm) REVERT: L 138 CYS cc_start: 0.8075 (t) cc_final: 0.7813 (t) REVERT: L 146 GLN cc_start: 0.9462 (OUTLIER) cc_final: 0.9189 (tm-30) REVERT: L 307 MET cc_start: 0.8726 (pmm) cc_final: 0.8510 (pmm) REVERT: L 366 GLN cc_start: 0.9562 (mm110) cc_final: 0.9280 (mm110) REVERT: N 166 MET cc_start: 0.9115 (mtt) cc_final: 0.8819 (mtp) REVERT: N 389 MET cc_start: 0.8460 (tmt) cc_final: 0.8213 (tmt) outliers start: 58 outliers final: 21 residues processed: 358 average time/residue: 1.4862 time to fit residues: 667.2231 Evaluate side-chains 345 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 312 time to evaluate : 4.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 354 GLU 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: 6.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 40.0000 chunk 413 optimal weight: 10.0000 chunk 173 optimal weight: 0.0770 chunk 704 optimal weight: 6.9990 chunk 584 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 6.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 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** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 54362 Z= 0.269 Angle : 0.528 9.580 73402 Z= 0.280 Chirality : 0.040 0.169 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.823 17.780 7728 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.11 % Allowed : 12.20 % Favored : 86.69 % 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: 2.01 (0.10), residues: 7308 helix: 2.30 (0.08), residues: 4228 sheet: 0.42 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.017 0.001 PHE B 204 TYR 0.012 0.001 TYR F 199 ARG 0.008 0.000 ARG H 362 *********************** 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 387 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 324 time to evaluate : 4.852 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: A 193 MET cc_start: 0.8612 (ptp) cc_final: 0.8325 (ptt) REVERT: A 352 GLN cc_start: 0.9308 (mm110) cc_final: 0.9079 (mm110) REVERT: B 16 MET cc_start: 0.8639 (mmm) cc_final: 0.8415 (mtm) REVERT: B 250 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (pp) REVERT: B 267 MET cc_start: 0.8408 (mmm) cc_final: 0.7854 (ptm) REVERT: B 520 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: C 389 MET cc_start: 0.9069 (tmm) cc_final: 0.8668 (tmm) REVERT: D 111 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8276 (mpm) REVERT: D 144 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9116 (mp) REVERT: D 164 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: D 267 MET cc_start: 0.8606 (mmm) cc_final: 0.8336 (mpp) REVERT: D 389 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8471 (tmt) REVERT: F 59 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8498 (mm-30) REVERT: F 114 MET cc_start: 0.8590 (mmm) cc_final: 0.8328 (mmm) REVERT: F 204 PHE cc_start: 0.8210 (m-80) cc_final: 0.7805 (m-80) REVERT: F 233 MET cc_start: 0.8444 (pmt) cc_final: 0.7850 (ppp) REVERT: F 520 MET cc_start: 0.8657 (mtp) cc_final: 0.8425 (mtp) REVERT: G 397 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8541 (mm-30) REVERT: H 193 MET cc_start: 0.8552 (ttm) cc_final: 0.8265 (ttm) REVERT: I 250 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8757 (pp) REVERT: I 307 MET cc_start: 0.8665 (pmm) cc_final: 0.8339 (pmm) REVERT: I 389 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (tmt) REVERT: J 233 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8527 (pmm) REVERT: J 250 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8219 (pp) REVERT: J 389 MET cc_start: 0.8867 (tmt) cc_final: 0.8612 (tmt) REVERT: K 44 PHE cc_start: 0.8052 (m-80) cc_final: 0.7820 (m-10) REVERT: K 307 MET cc_start: 0.8925 (mpm) cc_final: 0.8665 (mpm) REVERT: L 138 CYS cc_start: 0.8069 (t) cc_final: 0.7832 (t) REVERT: L 146 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9183 (tm-30) REVERT: L 366 GLN cc_start: 0.9563 (mm110) cc_final: 0.9276 (mm110) REVERT: N 111 MET cc_start: 0.8469 (mpp) cc_final: 0.7519 (mtm) REVERT: N 389 MET cc_start: 0.8478 (tmt) cc_final: 0.8222 (tmt) outliers start: 63 outliers final: 23 residues processed: 361 average time/residue: 1.4272 time to fit residues: 647.7791 Evaluate side-chains 341 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 307 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 517 THR 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 517 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 30.0000 chunk 514 optimal weight: 0.9990 chunk 398 optimal weight: 4.9990 chunk 592 optimal weight: 3.9990 chunk 393 optimal weight: 20.0000 chunk 701 optimal weight: 40.0000 chunk 439 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 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** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN L 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 54362 Z= 0.276 Angle : 0.537 9.897 73402 Z= 0.284 Chirality : 0.040 0.163 8932 Planarity : 0.003 0.032 9618 Dihedral : 3.831 18.014 7728 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.01 % Allowed : 13.07 % Favored : 85.93 % 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: 1.99 (0.10), residues: 7308 helix: 2.29 (0.08), residues: 4228 sheet: 0.39 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.018 0.001 PHE B 204 TYR 0.011 0.001 TYR N 476 ARG 0.006 0.000 ARG H 362 *********************** 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 372 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 315 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8612 (ptp) cc_final: 0.8323 (ptt) REVERT: A 352 GLN cc_start: 0.9293 (mm110) cc_final: 0.9071 (mm110) REVERT: B 69 MET cc_start: 0.8414 (mtt) cc_final: 0.8072 (mtp) REVERT: B 267 MET cc_start: 0.8345 (mmm) cc_final: 0.7786 (ptm) REVERT: B 520 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.6801 (mtm) REVERT: C 250 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8099 (pp) REVERT: C 389 MET cc_start: 0.9087 (tmm) cc_final: 0.8676 (tmm) REVERT: D 111 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8275 (mpm) REVERT: D 144 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9111 (mp) REVERT: D 164 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: D 267 MET cc_start: 0.8642 (mmm) cc_final: 0.8396 (mpp) REVERT: D 389 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8447 (tmt) REVERT: F 59 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8508 (mm-30) REVERT: F 114 MET cc_start: 0.8589 (mmm) cc_final: 0.8329 (mmm) REVERT: F 204 PHE cc_start: 0.8216 (m-80) cc_final: 0.7795 (m-80) REVERT: F 233 MET cc_start: 0.8410 (pmt) cc_final: 0.7870 (ppp) REVERT: F 520 MET cc_start: 0.8637 (mtp) cc_final: 0.8387 (mtp) REVERT: H 193 MET cc_start: 0.8522 (ttm) cc_final: 0.8241 (ttm) REVERT: I 73 MET cc_start: 0.8982 (ptp) cc_final: 0.8755 (ptm) REVERT: I 250 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8751 (pp) REVERT: I 307 MET cc_start: 0.8698 (pmm) cc_final: 0.8382 (pmm) REVERT: I 389 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8486 (tmt) REVERT: J 233 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8543 (pmm) REVERT: J 250 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8222 (pp) REVERT: J 288 MET cc_start: 0.8606 (mtm) cc_final: 0.8316 (ptp) REVERT: J 307 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: J 389 MET cc_start: 0.8884 (tmt) cc_final: 0.8624 (tmt) REVERT: K 44 PHE cc_start: 0.8057 (m-80) cc_final: 0.7831 (m-10) REVERT: K 307 MET cc_start: 0.8892 (mpm) cc_final: 0.8617 (mpm) REVERT: L 138 CYS cc_start: 0.8088 (t) cc_final: 0.7831 (t) REVERT: L 146 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9192 (tm-30) REVERT: L 307 MET cc_start: 0.8675 (pmm) cc_final: 0.8386 (pmm) REVERT: N 389 MET cc_start: 0.8483 (tmt) cc_final: 0.8224 (tmt) outliers start: 57 outliers final: 32 residues processed: 357 average time/residue: 1.4267 time to fit residues: 639.3568 Evaluate side-chains 351 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D 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 E residue 351 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 307 MET Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 354 GLU 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: 4.9990 chunk 419 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 446 optimal weight: 2.9990 chunk 478 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 551 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 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** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 54362 Z= 0.294 Angle : 0.555 11.913 73402 Z= 0.292 Chirality : 0.041 0.164 8932 Planarity : 0.003 0.038 9618 Dihedral : 3.841 18.059 7728 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.11 % Allowed : 13.38 % Favored : 85.50 % 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: 1.97 (0.10), residues: 7308 helix: 2.29 (0.08), residues: 4214 sheet: 0.36 (0.15), residues: 1064 loop : -0.24 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.020 0.001 PHE B 204 TYR 0.017 0.001 TYR B 360 ARG 0.008 0.000 ARG H 362 *********************** 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 380 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 317 time to evaluate : 4.715 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: A 193 MET cc_start: 0.8596 (ptp) cc_final: 0.8316 (ptt) REVERT: A 352 GLN cc_start: 0.9289 (mm110) cc_final: 0.9058 (mm110) REVERT: B 250 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 267 MET cc_start: 0.8347 (mmm) cc_final: 0.7690 (ptm) REVERT: B 520 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: C 250 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8106 (pp) REVERT: C 310 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.9048 (mp0) REVERT: C 389 MET cc_start: 0.9089 (tmm) cc_final: 0.8681 (tmm) REVERT: D 111 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8280 (mpm) REVERT: D 144 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9100 (mp) REVERT: D 164 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: D 267 MET cc_start: 0.8662 (mmm) cc_final: 0.8412 (mpp) REVERT: E 111 MET cc_start: 0.8757 (mpp) cc_final: 0.8231 (mpt) REVERT: F 59 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8523 (mm-30) REVERT: F 114 MET cc_start: 0.8591 (mmm) cc_final: 0.8331 (mmm) REVERT: F 204 PHE cc_start: 0.8225 (m-80) cc_final: 0.7815 (m-80) REVERT: F 233 MET cc_start: 0.8381 (pmt) cc_final: 0.7836 (ppp) REVERT: F 520 MET cc_start: 0.8605 (mtp) cc_final: 0.8316 (mtp) REVERT: H 193 MET cc_start: 0.8522 (ttm) cc_final: 0.8234 (ttm) REVERT: H 362 ARG cc_start: 0.9025 (ptp90) cc_final: 0.8617 (ptp90) REVERT: I 250 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8761 (pp) REVERT: I 307 MET cc_start: 0.8721 (pmm) cc_final: 0.8407 (pmm) REVERT: I 389 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8490 (tmt) REVERT: J 233 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (pmm) REVERT: J 250 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8233 (pp) REVERT: J 288 MET cc_start: 0.8628 (mtm) cc_final: 0.8279 (ptp) REVERT: J 389 MET cc_start: 0.8893 (tmt) cc_final: 0.8491 (tmt) REVERT: K 44 PHE cc_start: 0.8064 (m-80) cc_final: 0.7841 (m-10) REVERT: K 160 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9283 (tmmm) REVERT: K 307 MET cc_start: 0.8888 (mpm) cc_final: 0.8607 (mpm) REVERT: L 138 CYS cc_start: 0.8095 (t) cc_final: 0.7835 (t) REVERT: L 146 GLN cc_start: 0.9466 (OUTLIER) cc_final: 0.9192 (tm-30) REVERT: L 307 MET cc_start: 0.8620 (pmm) cc_final: 0.8325 (pmm) REVERT: N 389 MET cc_start: 0.8505 (tmt) cc_final: 0.8246 (tmt) outliers start: 63 outliers final: 29 residues processed: 362 average time/residue: 1.4224 time to fit residues: 649.5605 Evaluate side-chains 352 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 310 time to evaluate : 4.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 517 THR 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 517 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 354 GLU 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: 5.9990 chunk 613 optimal weight: 0.7980 chunk 653 optimal weight: 40.0000 chunk 393 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 590 optimal weight: 7.9990 chunk 618 optimal weight: 6.9990 chunk 651 optimal weight: 8.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 505 GLN ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 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: 0.8328 moved from start: 0.1463 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= 0.217 Angle : 0.547 13.408 73402 Z= 0.287 Chirality : 0.040 0.164 8932 Planarity : 0.003 0.040 9618 Dihedral : 3.830 17.775 7728 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.92 % Allowed : 13.77 % Favored : 85.31 % 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: 2.03 (0.10), residues: 7308 helix: 2.33 (0.08), residues: 4242 sheet: 0.36 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.024 0.001 PHE B 204 TYR 0.011 0.001 TYR N 476 ARG 0.005 0.000 ARG H 362 *********************** 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 368 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 316 time to evaluate : 4.794 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 166 MET cc_start: 0.8611 (mmm) cc_final: 0.8232 (tpt) REVERT: A 193 MET cc_start: 0.8603 (ptp) cc_final: 0.8177 (ptt) REVERT: A 352 GLN cc_start: 0.9281 (mm110) cc_final: 0.9059 (mm110) REVERT: B 250 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 267 MET cc_start: 0.8346 (mmm) cc_final: 0.7686 (ptm) REVERT: B 520 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: C 250 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (pp) REVERT: C 389 MET cc_start: 0.9090 (tmm) cc_final: 0.8679 (tmm) REVERT: D 111 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8247 (mpm) REVERT: D 144 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9094 (mp) REVERT: D 164 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: D 267 MET cc_start: 0.8648 (mmm) cc_final: 0.8413 (mpp) REVERT: E 111 MET cc_start: 0.8755 (mpp) cc_final: 0.8222 (mpt) REVERT: E 193 MET cc_start: 0.8255 (ppp) cc_final: 0.8018 (tmm) REVERT: F 59 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8464 (mm-30) REVERT: F 114 MET cc_start: 0.8587 (mmm) cc_final: 0.8328 (mmm) REVERT: F 204 PHE cc_start: 0.8228 (m-80) cc_final: 0.7764 (m-80) REVERT: F 389 MET cc_start: 0.6443 (tmt) cc_final: 0.6210 (tmm) REVERT: F 520 MET cc_start: 0.8566 (mtp) cc_final: 0.8248 (mtp) REVERT: H 193 MET cc_start: 0.8515 (ttm) cc_final: 0.8223 (ttm) REVERT: H 362 ARG cc_start: 0.9003 (ptp90) cc_final: 0.8738 (ptp90) REVERT: H 385 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8161 (p) REVERT: I 111 MET cc_start: 0.8593 (mpp) cc_final: 0.8027 (mtm) REVERT: I 250 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (pp) REVERT: I 307 MET cc_start: 0.8708 (pmm) cc_final: 0.8377 (pmm) REVERT: I 389 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8508 (tmt) REVERT: J 233 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (pmm) REVERT: J 250 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8274 (pp) REVERT: J 288 MET cc_start: 0.8647 (mtm) cc_final: 0.8223 (ptp) REVERT: J 389 MET cc_start: 0.8899 (tmt) cc_final: 0.8491 (tmt) REVERT: K 44 PHE cc_start: 0.8053 (m-80) cc_final: 0.7826 (m-10) REVERT: K 160 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9283 (tmmm) REVERT: K 307 MET cc_start: 0.8883 (mpm) cc_final: 0.8596 (mpm) REVERT: L 16 MET cc_start: 0.8711 (mtm) cc_final: 0.8494 (mtt) REVERT: L 138 CYS cc_start: 0.8106 (t) cc_final: 0.7843 (t) REVERT: L 146 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9180 (tm-30) REVERT: L 307 MET cc_start: 0.8671 (pmm) cc_final: 0.8358 (pmm) REVERT: N 166 MET cc_start: 0.9105 (mtt) cc_final: 0.8807 (mtp) REVERT: N 389 MET cc_start: 0.8491 (tmt) cc_final: 0.8238 (tmt) outliers start: 52 outliers final: 30 residues processed: 355 average time/residue: 1.4678 time to fit residues: 654.1961 Evaluate side-chains 347 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 304 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 9.9990 chunk 691 optimal weight: 8.9990 chunk 422 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 480 optimal weight: 4.9990 chunk 725 optimal weight: 6.9990 chunk 667 optimal weight: 6.9990 chunk 577 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 354 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 54362 Z= 0.264 Angle : 0.568 13.123 73402 Z= 0.297 Chirality : 0.041 0.187 8932 Planarity : 0.003 0.039 9618 Dihedral : 3.839 17.886 7728 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.80 % Allowed : 14.09 % Favored : 85.11 % 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: 1.98 (0.10), residues: 7308 helix: 2.29 (0.08), residues: 4228 sheet: 0.34 (0.15), residues: 1064 loop : -0.23 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.022 0.001 PHE B 204 TYR 0.018 0.001 TYR B 360 ARG 0.005 0.000 ARG H 362 ********************** 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 359 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 314 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9509 (tppt) cc_final: 0.9306 (tppt) REVERT: A 166 MET cc_start: 0.8591 (mmm) cc_final: 0.8215 (tpt) REVERT: A 193 MET cc_start: 0.8591 (ptp) cc_final: 0.8286 (ptt) REVERT: A 352 GLN cc_start: 0.9282 (mm110) cc_final: 0.9054 (mm110) REVERT: B 250 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8173 (pp) REVERT: B 267 MET cc_start: 0.8366 (mmm) cc_final: 0.7697 (ptm) REVERT: B 307 MET cc_start: 0.8618 (pmt) cc_final: 0.8043 (pmm) REVERT: B 520 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: C 250 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 389 MET cc_start: 0.9099 (tmm) cc_final: 0.8686 (tmm) REVERT: D 111 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8248 (mpm) REVERT: D 144 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9064 (mp) REVERT: D 164 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: D 267 MET cc_start: 0.8646 (mmm) cc_final: 0.8415 (mpp) REVERT: E 111 MET cc_start: 0.8768 (mpp) cc_final: 0.8244 (mpt) REVERT: E 193 MET cc_start: 0.8244 (ppp) cc_final: 0.7993 (tmm) REVERT: F 59 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8496 (mm-30) REVERT: F 114 MET cc_start: 0.8602 (mmm) cc_final: 0.8346 (mmm) REVERT: F 204 PHE cc_start: 0.8216 (m-80) cc_final: 0.7716 (m-80) REVERT: F 233 MET cc_start: 0.8587 (pmt) cc_final: 0.8082 (ppp) REVERT: F 520 MET cc_start: 0.8579 (mtp) cc_final: 0.8261 (mtp) REVERT: G 288 MET cc_start: 0.5685 (mtm) cc_final: 0.5320 (pp-130) REVERT: H 193 MET cc_start: 0.8521 (ttm) cc_final: 0.8226 (ttm) REVERT: H 362 ARG cc_start: 0.9005 (ptp90) cc_final: 0.8665 (ptp90) REVERT: H 385 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8154 (p) REVERT: I 250 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8705 (pp) REVERT: I 307 MET cc_start: 0.8709 (pmm) cc_final: 0.8375 (pmm) REVERT: I 389 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8508 (tmt) REVERT: J 233 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8486 (pmm) REVERT: J 250 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8249 (pp) REVERT: J 288 MET cc_start: 0.8646 (mtm) cc_final: 0.8195 (ptp) REVERT: J 389 MET cc_start: 0.8902 (tmt) cc_final: 0.8494 (tmt) REVERT: K 44 PHE cc_start: 0.8059 (m-80) cc_final: 0.7820 (m-10) REVERT: K 160 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9286 (tmmm) REVERT: K 307 MET cc_start: 0.8845 (mpm) cc_final: 0.8543 (mpm) REVERT: L 138 CYS cc_start: 0.8135 (t) cc_final: 0.7862 (t) REVERT: L 146 GLN cc_start: 0.9458 (OUTLIER) cc_final: 0.9188 (tm-30) REVERT: L 307 MET cc_start: 0.8608 (pmm) cc_final: 0.8362 (pmm) REVERT: N 389 MET cc_start: 0.8498 (tmt) cc_final: 0.8240 (tmt) outliers start: 45 outliers final: 27 residues processed: 344 average time/residue: 1.4639 time to fit residues: 630.5373 Evaluate side-chains 350 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 310 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 517 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 3.9990 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 0.4980 chunk 532 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 578 optimal weight: 0.5980 chunk 242 optimal weight: 40.0000 chunk 593 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.090245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061816 restraints weight = 155450.127| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.32 r_work: 0.3044 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54362 Z= 0.189 Angle : 0.552 12.885 73402 Z= 0.288 Chirality : 0.040 0.178 8932 Planarity : 0.003 0.033 9618 Dihedral : 3.808 17.535 7728 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.85 % Allowed : 14.13 % Favored : 85.02 % 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: 2.05 (0.10), residues: 7308 helix: 2.34 (0.08), residues: 4256 sheet: 0.35 (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 D 204 TYR 0.010 0.001 TYR C 478 ARG 0.007 0.000 ARG H 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13369.62 seconds wall clock time: 231 minutes 52.72 seconds (13912.72 seconds total)