Starting phenix.real_space_refine on Mon Apr 15 09:33:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn8_17778/04_2024/8pn8_17778_updated.pdb" } resolution = 2.31 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= 0.032 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 21066 2.51 5 N 5928 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34298 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "H" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "I" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "J" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "K" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "L" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "F" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 17.51, per 1000 atoms: 0.51 Number of scatterers: 34298 At special positions: 0 Unit cell: (151.497, 152.334, 138.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 7136 8.00 N 5928 7.00 C 21066 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 - 3.50 Amino acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.04 Conformation dependent library (CDL) restraints added in 5.9 seconds 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 39 sheets defined 35.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 136 through 153 Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.698A pdb=" N VAL A 172 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.896A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.580A pdb=" N ILE A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 479 through 495 removed outlier: 5.166A pdb=" N ARG A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 495 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 136 through 153 Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.682A pdb=" N VAL B 172 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.500A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.671A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 479 through 495 removed outlier: 5.116A pdb=" N ARG B 483 " --> pdb=" O HIS B 480 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 136 through 153 Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.680A pdb=" N VAL C 172 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.678A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.568A pdb=" N ILE C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 479 through 495 removed outlier: 5.091A pdb=" N ARG C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 494 " --> pdb=" O GLY C 491 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR C 495 " --> pdb=" O MET C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 136 through 153 Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.640A pdb=" N VAL D 172 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.657A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.625A pdb=" N ILE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 479 through 495 removed outlier: 5.164A pdb=" N ARG D 483 " --> pdb=" O HIS D 480 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR D 495 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 21 through 29 Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 102 through 118 Processing helix chain 'E' and resid 136 through 153 removed outlier: 3.598A pdb=" N ALA E 139 " --> pdb=" O GLY E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 removed outlier: 3.663A pdb=" N VAL E 172 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 173 " --> pdb=" O GLY E 170 " (cutoff:3.500A) Proline residue: E 175 - end of helix Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.646A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.601A pdb=" N ILE E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 432 through 439 Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'E' and resid 479 through 495 removed outlier: 5.162A pdb=" N ARG E 483 " --> pdb=" O HIS E 480 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG E 494 " --> pdb=" O GLY E 491 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR E 495 " --> pdb=" O MET E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 16 Processing helix chain 'F' and resid 21 through 29 Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 102 through 118 Processing helix chain 'F' and resid 133 through 153 removed outlier: 6.656A pdb=" N VAL F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 139 " --> pdb=" O GLY F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.700A pdb=" N VAL F 172 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Proline residue: F 175 - end of helix Processing helix chain 'F' and resid 195 through 202 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 267 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.907A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.587A pdb=" N ILE F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 439 Processing helix chain 'F' and resid 448 through 461 Processing helix chain 'F' and resid 465 through 469 Processing helix chain 'F' and resid 479 through 495 removed outlier: 5.108A pdb=" N ARG F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 494 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR F 495 " --> pdb=" O MET F 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 484 removed outlier: 3.765A pdb=" N GLY G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 588 removed outlier: 3.654A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 484 removed outlier: 3.823A pdb=" N GLY H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 494 No H-bonds generated for 'chain 'H' and resid 492 through 494' Processing helix chain 'H' and resid 580 through 588 removed outlier: 3.640A pdb=" N LEU H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 484 removed outlier: 3.765A pdb=" N GLY I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 494 No H-bonds generated for 'chain 'I' and resid 492 through 494' Processing helix chain 'I' and resid 580 through 588 removed outlier: 3.656A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 484 removed outlier: 3.757A pdb=" N GLY J 484 " --> pdb=" O ILE J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 494 No H-bonds generated for 'chain 'J' and resid 492 through 494' Processing helix chain 'J' and resid 580 through 588 removed outlier: 3.660A pdb=" N LEU J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 484 removed outlier: 3.812A pdb=" N GLY K 484 " --> pdb=" O ILE K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 494 No H-bonds generated for 'chain 'K' and resid 492 through 494' Processing helix chain 'K' and resid 580 through 588 removed outlier: 3.836A pdb=" N LEU K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 484 removed outlier: 3.838A pdb=" N GLY L 484 " --> pdb=" O ILE L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 588 removed outlier: 3.640A pdb=" N LEU L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.406A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE A 89 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 123 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS A 91 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A 125 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE A 180 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 163 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 182 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 226 " --> pdb=" O MET A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.128A pdb=" N TYR A 189 " --> pdb=" O CYS A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.359A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 418 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 397 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR A 420 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A 475 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.109A pdb=" N GLN A 426 " --> pdb=" O ALA A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.404A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N PHE B 89 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 123 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LYS B 91 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE B 125 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 180 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 163 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 182 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY B 226 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.129A pdb=" N TYR B 189 " --> pdb=" O CYS B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 296 through 299 removed outlier: 4.357A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 418 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE B 397 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR B 420 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU B 475 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.078A pdb=" N GLN B 426 " --> pdb=" O ALA B 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.427A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 89 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 123 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS C 91 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE C 125 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE C 180 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE C 163 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 182 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 226 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.093A pdb=" N TYR C 189 " --> pdb=" O CYS C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.347A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 418 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 397 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR C 420 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 475 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.421A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE D 89 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 123 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS D 91 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 125 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE D 180 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE D 163 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 182 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY D 226 " --> pdb=" O MET D 183 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.093A pdb=" N TYR D 189 " --> pdb=" O CYS D 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 296 through 299 removed outlier: 4.400A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU D 418 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 397 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR D 420 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.423A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N PHE E 89 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE E 123 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS E 91 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE E 125 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE E 180 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE E 163 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE E 182 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY E 226 " --> pdb=" O MET E 183 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.117A pdb=" N TYR E 189 " --> pdb=" O CYS E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 296 through 299 removed outlier: 4.396A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 418 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE E 397 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR E 420 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.432A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE F 89 " --> pdb=" O PRO F 121 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE F 123 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS F 91 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE F 125 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE F 180 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE F 163 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE F 182 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY F 226 " --> pdb=" O MET F 183 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.098A pdb=" N TYR F 189 " --> pdb=" O CYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 296 through 299 removed outlier: 4.348A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F 418 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE F 397 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR F 420 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU F 475 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 509 through 513 removed outlier: 3.843A pdb=" N GLN G 551 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 600 through 602 removed outlier: 3.599A pdb=" N LEU G 664 " --> pdb=" O LEU G 601 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 608 through 611 removed outlier: 6.753A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE G 628 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN G 636 " --> pdb=" O ILE G 628 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 509 through 513 removed outlier: 3.869A pdb=" N GLN H 551 " --> pdb=" O VAL H 548 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 600 through 603 removed outlier: 3.886A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS H 603 " --> pdb=" O VAL H 662 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 662 " --> pdb=" O CYS H 603 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 608 through 612 removed outlier: 6.455A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE H 628 " --> pdb=" O ASN H 636 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN H 636 " --> pdb=" O ILE H 628 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 509 through 513 removed outlier: 3.872A pdb=" N GLN I 551 " --> pdb=" O VAL I 548 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 600 through 603 removed outlier: 3.979A pdb=" N LEU I 664 " --> pdb=" O LEU I 601 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS I 603 " --> pdb=" O VAL I 662 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL I 662 " --> pdb=" O CYS I 603 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 608 through 611 removed outlier: 6.585A pdb=" N ILE I 628 " --> pdb=" O LYS I 610 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU I 630 " --> pdb=" O MET I 634 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET I 634 " --> pdb=" O GLU I 630 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 509 through 513 removed outlier: 3.841A pdb=" N GLN J 551 " --> pdb=" O VAL J 548 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 600 through 603 removed outlier: 3.917A pdb=" N LEU J 664 " --> pdb=" O LEU J 601 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS J 603 " --> pdb=" O VAL J 662 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL J 662 " --> pdb=" O CYS J 603 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 608 through 612 removed outlier: 6.606A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU J 638 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE J 628 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN J 636 " --> pdb=" O ILE J 628 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 509 through 513 removed outlier: 3.853A pdb=" N GLN K 551 " --> pdb=" O VAL K 548 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 618 through 620 removed outlier: 3.705A pdb=" N GLN K 618 " --> pdb=" O ILE K 646 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 608 through 612 removed outlier: 6.646A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU K 630 " --> pdb=" O MET K 634 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET K 634 " --> pdb=" O GLU K 630 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 508 through 513 removed outlier: 3.881A pdb=" N GLN L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 618 through 620 removed outlier: 3.609A pdb=" N GLN L 618 " --> pdb=" O ILE L 646 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 620 " --> pdb=" O GLY L 644 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY L 644 " --> pdb=" O VAL L 620 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 600 through 603 removed outlier: 3.833A pdb=" N LEU L 664 " --> pdb=" O LEU L 601 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS L 603 " --> pdb=" O VAL L 662 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL L 662 " --> pdb=" O CYS L 603 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 608 through 612 removed outlier: 6.629A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU L 638 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE L 628 " --> pdb=" O ASN L 636 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN L 636 " --> pdb=" O ILE L 628 " (cutoff:3.500A) 1302 hydrogen bonds defined for protein. 3225 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: 15.32 Time building geometry restraints manager: 14.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.73: 33762 1.73 - 2.24: 276 2.24 - 2.75: 0 2.75 - 3.27: 6 3.27 - 3.78: 6 Bond restraints: 34050 Sorted by residual: bond pdb=" AP1 COA B 601 " pdb="AO5* COA B 601 " ideal model delta sigma weight residual 1.610 3.782 -2.172 2.00e-02 2.50e+03 1.18e+04 bond pdb=" AP1 COA C 601 " pdb="AO5* COA C 601 " ideal model delta sigma weight residual 1.610 3.779 -2.169 2.00e-02 2.50e+03 1.18e+04 bond pdb=" AP1 COA F 601 " pdb="AO5* COA F 601 " ideal model delta sigma weight residual 1.610 3.777 -2.167 2.00e-02 2.50e+03 1.17e+04 bond pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " ideal model delta sigma weight residual 1.610 3.777 -2.167 2.00e-02 2.50e+03 1.17e+04 bond pdb=" AP1 COA D 601 " pdb="AO5* COA D 601 " ideal model delta sigma weight residual 1.610 3.740 -2.130 2.00e-02 2.50e+03 1.13e+04 ... (remaining 34045 not shown) Histogram of bond angle deviations from ideal: 34.54 - 58.71: 10 58.71 - 82.87: 8 82.87 - 107.03: 1133 107.03 - 131.20: 44816 131.20 - 155.36: 95 Bond angle restraints: 46062 Sorted by residual: angle pdb=" AO3 COA B 601 " pdb=" AP1 COA B 601 " pdb="AO5* COA B 601 " ideal model delta sigma weight residual 102.60 34.54 68.06 3.00e+00 1.11e-01 5.15e+02 angle pdb=" AO3 COA C 601 " pdb=" AP1 COA C 601 " pdb="AO5* COA C 601 " ideal model delta sigma weight residual 102.60 34.74 67.86 3.00e+00 1.11e-01 5.12e+02 angle pdb=" AO3 COA A 601 " pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " ideal model delta sigma weight residual 102.60 34.88 67.72 3.00e+00 1.11e-01 5.10e+02 angle pdb=" AO3 COA F 601 " pdb=" AP1 COA F 601 " pdb="AO5* COA F 601 " ideal model delta sigma weight residual 102.60 34.90 67.70 3.00e+00 1.11e-01 5.09e+02 angle pdb=" AO3 COA E 601 " pdb=" AP1 COA E 601 " pdb="AO5* COA E 601 " ideal model delta sigma weight residual 102.60 36.23 66.37 3.00e+00 1.11e-01 4.89e+02 ... (remaining 46057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 20074 22.62 - 45.24: 427 45.24 - 67.86: 73 67.86 - 90.47: 40 90.47 - 113.09: 14 Dihedral angle restraints: 20628 sinusoidal: 8442 harmonic: 12186 Sorted by residual: dihedral pdb=" AO3 COA D 601 " pdb=" AO6 COA D 601 " pdb=" AP2 COA D 601 " pdb="PC12 COA D 601 " ideal model delta sinusoidal sigma weight residual -81.62 31.47 -113.09 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" AO3 COA E 601 " pdb=" AO6 COA E 601 " pdb=" AP2 COA E 601 " pdb="PC12 COA E 601 " ideal model delta sinusoidal sigma weight residual -81.62 31.05 -112.67 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" AO3 COA C 601 " pdb=" AO6 COA C 601 " pdb=" AP2 COA C 601 " pdb="PC12 COA C 601 " ideal model delta sinusoidal sigma weight residual -81.62 28.74 -110.36 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 20625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4266 0.057 - 0.115: 774 0.115 - 0.172: 80 0.172 - 0.229: 10 0.229 - 0.287: 12 Chirality restraints: 5142 Sorted by residual: chirality pdb="AC2* COA B 601 " pdb="AC1* COA B 601 " pdb="AC3* COA B 601 " pdb="AO2* COA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb="AC2* COA D 601 " pdb="AC1* COA D 601 " pdb="AC3* COA D 601 " pdb="AO2* COA D 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb="AC2* COA E 601 " pdb="AC1* COA E 601 " pdb="AC3* COA E 601 " pdb="AO2* COA E 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 5139 not shown) Planarity restraints: 6048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 366 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 500 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO F 501 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 501 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 501 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 538 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.21e+00 pdb=" N PRO K 539 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO K 539 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 539 " -0.015 5.00e-02 4.00e+02 ... (remaining 6045 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 23 2.27 - 2.92: 14303 2.92 - 3.58: 50739 3.58 - 4.24: 89955 4.24 - 4.90: 146662 Nonbonded interactions: 301682 Sorted by model distance: nonbonded pdb=" AP2 COA C 601 " pdb="AO5* COA C 601 " model vdw 1.608 2.720 nonbonded pdb=" AP2 COA E 601 " pdb="AO5* COA E 601 " model vdw 1.608 2.720 nonbonded pdb=" AP2 COA B 601 " pdb="AO5* COA B 601 " model vdw 1.609 2.720 nonbonded pdb=" AP2 COA D 601 " pdb="AO5* COA D 601 " model vdw 1.609 2.720 nonbonded pdb=" AP2 COA A 601 " pdb="AO5* COA A 601 " model vdw 1.609 2.720 ... (remaining 301677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 27.630 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 90.660 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.035 2.172 34050 Z= 2.200 Angle : 1.372 68.055 46062 Z= 0.490 Chirality : 0.046 0.287 5142 Planarity : 0.003 0.029 6048 Dihedral : 11.042 113.093 12804 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.43 % Allowed : 3.51 % Favored : 96.06 % 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: 0.98 (0.13), residues: 4290 helix: 1.15 (0.13), residues: 1548 sheet: 1.69 (0.18), residues: 750 loop : -0.10 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 537 HIS 0.008 0.001 HIS B 104 PHE 0.013 0.001 PHE I 578 TYR 0.007 0.001 TYR B 173 ARG 0.002 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 663 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 648 time to evaluate : 4.113 Fit side-chains REVERT: A 6 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 21 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6981 (mp0) REVERT: A 29 LYS cc_start: 0.8196 (tppt) cc_final: 0.7887 (mmmt) REVERT: A 171 ASP cc_start: 0.8675 (m-30) cc_final: 0.8017 (t0) REVERT: A 190 MET cc_start: 0.9030 (mtp) cc_final: 0.8780 (mtp) REVERT: A 267 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8157 (mmtp) REVERT: A 317 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: A 400 LYS cc_start: 0.8406 (mttt) cc_final: 0.8138 (mtmp) REVERT: B 6 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7200 (mt-10) REVERT: B 21 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7385 (mt-10) REVERT: B 22 LYS cc_start: 0.7810 (tttt) cc_final: 0.7523 (ttpt) REVERT: B 171 ASP cc_start: 0.8707 (m-30) cc_final: 0.7998 (t0) REVERT: B 190 MET cc_start: 0.8977 (mtp) cc_final: 0.8712 (mtp) REVERT: B 220 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8601 (mtmm) REVERT: B 289 ARG cc_start: 0.8415 (mmt180) cc_final: 0.8129 (mtp85) REVERT: B 317 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.8005 (mtt-85) REVERT: B 400 LYS cc_start: 0.8439 (mttt) cc_final: 0.8198 (mtmp) REVERT: B 449 LYS cc_start: 0.7778 (tptt) cc_final: 0.7518 (tptm) REVERT: B 502 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7682 (ttm110) REVERT: C 6 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6549 (pm20) REVERT: C 22 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7604 (ttpt) REVERT: C 171 ASP cc_start: 0.8532 (m-30) cc_final: 0.8146 (t0) REVERT: C 266 ASP cc_start: 0.8346 (t0) cc_final: 0.7996 (t0) REVERT: C 289 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8299 (mtp85) REVERT: C 449 LYS cc_start: 0.7824 (tptt) cc_final: 0.7448 (tptm) REVERT: C 452 GLU cc_start: 0.7703 (tt0) cc_final: 0.7252 (tt0) REVERT: C 453 ARG cc_start: 0.6586 (mtt-85) cc_final: 0.6362 (mmt90) REVERT: C 456 GLU cc_start: 0.7276 (pt0) cc_final: 0.7060 (pt0) REVERT: C 458 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7456 (tp30) REVERT: C 502 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7722 (ttm170) REVERT: D 6 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7200 (mt-10) REVERT: D 21 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6992 (mp0) REVERT: D 22 LYS cc_start: 0.7971 (tttm) cc_final: 0.7657 (ttpt) REVERT: D 171 ASP cc_start: 0.8676 (m-30) cc_final: 0.8080 (t0) REVERT: D 400 LYS cc_start: 0.8347 (mttt) cc_final: 0.8099 (mtmp) REVERT: D 449 LYS cc_start: 0.7796 (tptt) cc_final: 0.7580 (tptm) REVERT: D 453 ARG cc_start: 0.6775 (mtt-85) cc_final: 0.6176 (mtt180) REVERT: D 475 GLU cc_start: 0.8414 (tp30) cc_final: 0.7739 (tp30) REVERT: D 502 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7660 (ttm110) REVERT: E 22 LYS cc_start: 0.7971 (tttt) cc_final: 0.7474 (ttpt) REVERT: E 66 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8497 (ptpp) REVERT: E 67 GLN cc_start: 0.8369 (pt0) cc_final: 0.8169 (pt0) REVERT: E 220 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8591 (mtmm) REVERT: E 268 SER cc_start: 0.9015 (m) cc_final: 0.8795 (t) REVERT: E 400 LYS cc_start: 0.8336 (mttt) cc_final: 0.8077 (mtmp) REVERT: E 452 GLU cc_start: 0.7622 (tt0) cc_final: 0.7147 (tt0) REVERT: F 6 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6527 (pm20) REVERT: F 21 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6814 (mp0) REVERT: F 22 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7182 (pptt) REVERT: F 29 LYS cc_start: 0.8286 (mmtp) cc_final: 0.8072 (mmmt) REVERT: F 30 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7834 (mtm-85) REVERT: F 171 ASP cc_start: 0.8501 (m-30) cc_final: 0.8112 (t0) REVERT: F 189 TYR cc_start: 0.8710 (p90) cc_final: 0.8509 (p90) REVERT: F 266 ASP cc_start: 0.8565 (t0) cc_final: 0.8359 (t0) REVERT: F 400 LYS cc_start: 0.8343 (mttt) cc_final: 0.8117 (mtmp) REVERT: F 453 ARG cc_start: 0.7365 (mmt180) cc_final: 0.6417 (mtt180) REVERT: F 458 GLU cc_start: 0.7603 (tt0) cc_final: 0.7162 (tp30) REVERT: F 502 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7706 (ttm170) REVERT: G 483 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7931 (mmm160) REVERT: G 490 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8006 (ptp-170) REVERT: G 635 GLU cc_start: 0.6127 (mt-10) cc_final: 0.4682 (pt0) REVERT: H 483 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7823 (mmm160) REVERT: H 490 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8049 (ptp-170) REVERT: H 520 ASP cc_start: 0.7002 (p0) cc_final: 0.6637 (p0) REVERT: H 534 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7724 (mtp85) REVERT: H 580 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8179 (mmt-90) REVERT: H 630 GLU cc_start: 0.7022 (tt0) cc_final: 0.6733 (tt0) REVERT: H 635 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5308 (pt0) REVERT: I 483 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7588 (mmm160) REVERT: I 489 MET cc_start: 0.8883 (ttp) cc_final: 0.8672 (ttp) REVERT: I 630 GLU cc_start: 0.7009 (tt0) cc_final: 0.6676 (tt0) REVERT: J 483 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8025 (mmm160) REVERT: J 490 ARG cc_start: 0.8322 (ptp90) cc_final: 0.7965 (ptp-170) REVERT: K 483 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7818 (mmm160) REVERT: K 490 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7979 (ptp-170) REVERT: K 534 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7409 (ttm110) REVERT: K 613 MET cc_start: 0.5061 (mpp) cc_final: 0.2645 (tmt) REVERT: K 635 GLU cc_start: 0.5736 (mt-10) cc_final: 0.4529 (pt0) REVERT: K 665 GLU cc_start: 0.5004 (mt-10) cc_final: 0.4591 (mm-30) REVERT: L 483 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7619 (mmm160) REVERT: L 632 MET cc_start: 0.6827 (mtm) cc_final: 0.6290 (mtm) REVERT: L 635 GLU cc_start: 0.6008 (mt-10) cc_final: 0.4863 (pt0) outliers start: 15 outliers final: 6 residues processed: 660 average time/residue: 2.0530 time to fit residues: 1553.3646 Evaluate side-chains 525 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 519 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 203 optimal weight: 0.0980 chunk 248 optimal weight: 0.5980 chunk 386 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 278 ASN G 479 ASN G 556 GLN H 479 ASN H 556 GLN I 476 HIS I 479 ASN I 556 GLN J 479 ASN J 556 GLN K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34050 Z= 0.145 Angle : 0.505 6.994 46062 Z= 0.256 Chirality : 0.043 0.139 5142 Planarity : 0.004 0.039 6048 Dihedral : 10.092 151.668 4936 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.86 % Allowed : 8.84 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.13), residues: 4290 helix: 0.92 (0.13), residues: 1506 sheet: 1.39 (0.17), residues: 792 loop : 0.20 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 544 HIS 0.007 0.001 HIS C 104 PHE 0.011 0.001 PHE C 384 TYR 0.008 0.001 TYR E 173 ARG 0.005 0.000 ARG I 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 564 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 500 time to evaluate : 3.838 Fit side-chains REVERT: A 21 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7004 (mp0) REVERT: A 29 LYS cc_start: 0.8208 (tppt) cc_final: 0.7900 (mmmt) REVERT: A 171 ASP cc_start: 0.8502 (m-30) cc_final: 0.7801 (t0) REVERT: A 257 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 317 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.7956 (mtp85) REVERT: A 400 LYS cc_start: 0.8397 (mttt) cc_final: 0.8134 (mtmp) REVERT: B 21 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7422 (mt-10) REVERT: B 22 LYS cc_start: 0.7889 (tttt) cc_final: 0.7417 (ttpt) REVERT: B 30 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7935 (mtm-85) REVERT: B 171 ASP cc_start: 0.8560 (m-30) cc_final: 0.7831 (t0) REVERT: B 190 MET cc_start: 0.9000 (mtp) cc_final: 0.8732 (mtp) REVERT: B 196 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: B 220 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8617 (mtmm) REVERT: B 289 ARG cc_start: 0.8440 (mmt180) cc_final: 0.8158 (mtp85) REVERT: B 317 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.7812 (mtm180) REVERT: B 400 LYS cc_start: 0.8420 (mttt) cc_final: 0.8179 (mtmp) REVERT: B 430 MET cc_start: 0.9154 (ptp) cc_final: 0.8942 (ptm) REVERT: B 502 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7681 (ttm110) REVERT: C 6 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6597 (pm20) REVERT: C 9 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7272 (mm-30) REVERT: C 22 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7664 (ttpt) REVERT: C 49 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: C 171 ASP cc_start: 0.8445 (m-30) cc_final: 0.7973 (t0) REVERT: C 257 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: C 266 ASP cc_start: 0.8436 (t0) cc_final: 0.8050 (t0) REVERT: C 289 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8288 (mtp85) REVERT: C 449 LYS cc_start: 0.7824 (tptt) cc_final: 0.7510 (tptm) REVERT: C 452 GLU cc_start: 0.7694 (tt0) cc_final: 0.7252 (tt0) REVERT: C 455 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7076 (tmmm) REVERT: C 456 GLU cc_start: 0.7250 (pt0) cc_final: 0.7031 (pt0) REVERT: C 458 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7494 (tp30) REVERT: C 497 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: C 502 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7712 (ttm170) REVERT: D 21 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7023 (mp0) REVERT: D 22 LYS cc_start: 0.7996 (tttm) cc_final: 0.7673 (ttpt) REVERT: D 257 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: D 400 LYS cc_start: 0.8346 (mttt) cc_final: 0.8141 (mtmp) REVERT: D 453 ARG cc_start: 0.6827 (mtt-85) cc_final: 0.6245 (mtt180) REVERT: D 475 GLU cc_start: 0.8409 (tp30) cc_final: 0.7709 (tp30) REVERT: D 502 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7642 (ttm110) REVERT: E 22 LYS cc_start: 0.8076 (tttt) cc_final: 0.7582 (ttpt) REVERT: E 220 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8599 (mtmm) REVERT: E 400 LYS cc_start: 0.8322 (mttt) cc_final: 0.8111 (mtmp) REVERT: F 6 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6583 (pm20) REVERT: F 9 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7230 (mm-30) REVERT: F 21 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6835 (mp0) REVERT: F 22 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7263 (pptt) REVERT: F 29 LYS cc_start: 0.8339 (mmtp) cc_final: 0.8106 (mmmt) REVERT: F 30 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7774 (mtm-85) REVERT: F 49 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: F 171 ASP cc_start: 0.8423 (m-30) cc_final: 0.7944 (t0) REVERT: F 257 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: F 266 ASP cc_start: 0.8561 (t0) cc_final: 0.8348 (t0) REVERT: F 400 LYS cc_start: 0.8328 (mttt) cc_final: 0.8113 (mtmp) REVERT: F 453 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6419 (mtt180) REVERT: F 458 GLU cc_start: 0.7558 (tt0) cc_final: 0.7154 (tp30) REVERT: G 483 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7899 (mmm160) REVERT: G 630 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.5558 (tm-30) REVERT: G 635 GLU cc_start: 0.5657 (mt-10) cc_final: 0.4661 (pt0) REVERT: H 483 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7794 (mmm160) REVERT: H 490 ARG cc_start: 0.8260 (ptp90) cc_final: 0.8057 (ptp-170) REVERT: H 517 ASP cc_start: 0.7765 (p0) cc_final: 0.7477 (p0) REVERT: H 534 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7694 (mtp85) REVERT: H 580 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8185 (mmt-90) REVERT: H 630 GLU cc_start: 0.6778 (tt0) cc_final: 0.6512 (tt0) REVERT: H 635 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5266 (pt0) REVERT: I 483 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7584 (mmm160) REVERT: I 520 ASP cc_start: 0.6368 (m-30) cc_final: 0.6033 (m-30) REVERT: I 527 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7509 (p0) REVERT: I 534 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7257 (mtp85) REVERT: I 630 GLU cc_start: 0.6754 (tt0) cc_final: 0.6473 (tt0) REVERT: J 483 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8028 (mmm160) REVERT: J 630 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: K 483 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7809 (mmm160) REVERT: K 490 ARG cc_start: 0.8283 (ptp90) cc_final: 0.7995 (ptp-170) REVERT: K 613 MET cc_start: 0.5025 (mpp) cc_final: 0.2660 (tmt) REVERT: K 630 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: K 635 GLU cc_start: 0.5603 (mt-10) cc_final: 0.4529 (pt0) REVERT: K 665 GLU cc_start: 0.5004 (mt-10) cc_final: 0.4604 (mm-30) REVERT: L 483 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7630 (mmm160) REVERT: L 635 GLU cc_start: 0.5531 (mt-10) cc_final: 0.4941 (pt0) outliers start: 64 outliers final: 26 residues processed: 524 average time/residue: 2.0849 time to fit residues: 1251.6965 Evaluate side-chains 524 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 485 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 527 ASP Chi-restraints excluded: chain L residue 552 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 321 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 387 optimal weight: 3.9990 chunk 418 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 chunk 384 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 310 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN C 276 ASN E 67 GLN F 278 ASN G 479 ASN G 556 GLN H 479 ASN I 479 ASN I 556 GLN J 479 ASN J 556 GLN K 476 HIS K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.005 0.051 34050 Z= 0.357 Angle : 0.580 6.811 46062 Z= 0.303 Chirality : 0.049 0.183 5142 Planarity : 0.005 0.039 6048 Dihedral : 10.422 173.003 4936 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.32 % Allowed : 9.36 % Favored : 88.32 % 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: 0.60 (0.13), residues: 4290 helix: 0.49 (0.13), residues: 1488 sheet: 1.30 (0.17), residues: 792 loop : 0.08 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 537 HIS 0.012 0.002 HIS B 104 PHE 0.016 0.002 PHE E 384 TYR 0.015 0.002 TYR F 173 ARG 0.009 0.001 ARG K 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 557 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 477 time to evaluate : 3.842 Fit side-chains REVERT: A 21 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6953 (mp0) REVERT: A 29 LYS cc_start: 0.8296 (tppt) cc_final: 0.7948 (mmmt) REVERT: A 171 ASP cc_start: 0.8462 (m-30) cc_final: 0.7951 (t0) REVERT: A 196 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: A 257 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: A 267 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8191 (mmtp) REVERT: A 285 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: A 317 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.7930 (mtp85) REVERT: A 400 LYS cc_start: 0.8534 (mttt) cc_final: 0.8178 (mtmp) REVERT: B 21 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7068 (mp0) REVERT: B 22 LYS cc_start: 0.7931 (tttt) cc_final: 0.7446 (ttpt) REVERT: B 171 ASP cc_start: 0.8522 (m-30) cc_final: 0.7942 (t0) REVERT: B 190 MET cc_start: 0.9255 (mtp) cc_final: 0.9006 (mtp) REVERT: B 196 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: B 220 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8609 (mtmt) REVERT: B 257 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 266 ASP cc_start: 0.8314 (t70) cc_final: 0.7839 (t0) REVERT: B 267 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8212 (mmtp) REVERT: B 289 ARG cc_start: 0.8489 (mmt180) cc_final: 0.8194 (mtp85) REVERT: B 317 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.7796 (mtm180) REVERT: B 400 LYS cc_start: 0.8574 (mttt) cc_final: 0.8247 (mtmp) REVERT: B 452 GLU cc_start: 0.7926 (tt0) cc_final: 0.7641 (pt0) REVERT: C 6 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6491 (pm20) REVERT: C 9 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 21 GLU cc_start: 0.7839 (tp30) cc_final: 0.7407 (mp0) REVERT: C 22 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7734 (ttpt) REVERT: C 49 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: C 171 ASP cc_start: 0.8478 (m-30) cc_final: 0.8108 (t0) REVERT: C 257 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: C 400 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8393 (mtmp) REVERT: C 449 LYS cc_start: 0.7849 (tptt) cc_final: 0.7619 (tptm) REVERT: C 452 GLU cc_start: 0.7712 (tt0) cc_final: 0.7394 (tt0) REVERT: C 453 ARG cc_start: 0.7126 (mpt-90) cc_final: 0.6709 (mtt180) REVERT: C 455 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7094 (tmmm) REVERT: C 458 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7472 (tp30) REVERT: C 475 GLU cc_start: 0.8352 (tp30) cc_final: 0.7934 (tp30) REVERT: C 497 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: C 502 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7756 (ttm170) REVERT: D 21 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7042 (mp0) REVERT: D 22 LYS cc_start: 0.8215 (tttm) cc_final: 0.7909 (ttpt) REVERT: D 257 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: D 400 LYS cc_start: 0.8447 (mttt) cc_final: 0.8189 (mtmp) REVERT: D 452 GLU cc_start: 0.7948 (tt0) cc_final: 0.7680 (pt0) REVERT: D 453 ARG cc_start: 0.6847 (mtt-85) cc_final: 0.6264 (mtt180) REVERT: D 475 GLU cc_start: 0.8452 (tp30) cc_final: 0.7868 (tp30) REVERT: E 22 LYS cc_start: 0.8116 (tttt) cc_final: 0.7613 (ttpt) REVERT: E 220 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8664 (mtmm) REVERT: E 257 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: E 400 LYS cc_start: 0.8441 (mttt) cc_final: 0.8167 (mtmp) REVERT: F 6 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6502 (pm20) REVERT: F 9 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7029 (mm-30) REVERT: F 21 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6847 (mp0) REVERT: F 22 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7328 (pptt) REVERT: F 29 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8162 (mmmt) REVERT: F 49 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: F 171 ASP cc_start: 0.8462 (m-30) cc_final: 0.8083 (t0) REVERT: F 257 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: F 266 ASP cc_start: 0.8684 (t0) cc_final: 0.8470 (t0) REVERT: F 400 LYS cc_start: 0.8554 (mttt) cc_final: 0.8256 (mtmp) REVERT: F 453 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6409 (mtt180) REVERT: F 458 GLU cc_start: 0.7591 (tt0) cc_final: 0.7177 (tp30) REVERT: G 483 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7883 (mmm160) REVERT: G 630 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.5490 (tm-30) REVERT: G 635 GLU cc_start: 0.5681 (mt-10) cc_final: 0.4722 (pt0) REVERT: H 483 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7835 (mmm160) REVERT: H 490 ARG cc_start: 0.8355 (ptp90) cc_final: 0.8123 (ptp-170) REVERT: H 580 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8243 (mmt-90) REVERT: H 630 GLU cc_start: 0.6770 (tt0) cc_final: 0.6534 (tt0) REVERT: H 635 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5384 (pt0) REVERT: I 483 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7576 (mmm160) REVERT: I 520 ASP cc_start: 0.6334 (m-30) cc_final: 0.5939 (m-30) REVERT: I 527 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7584 (p0) REVERT: I 534 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7302 (mtp85) REVERT: I 630 GLU cc_start: 0.6835 (tt0) cc_final: 0.6546 (tt0) REVERT: J 483 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8038 (mmm160) REVERT: J 630 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5540 (tm-30) REVERT: K 483 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7827 (mmm160) REVERT: K 613 MET cc_start: 0.5059 (mpp) cc_final: 0.2580 (tmt) REVERT: K 630 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5642 (tm-30) REVERT: K 635 GLU cc_start: 0.5625 (mt-10) cc_final: 0.4551 (pt0) REVERT: K 665 GLU cc_start: 0.5009 (mt-10) cc_final: 0.4629 (mm-30) REVERT: L 483 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7646 (mmm160) REVERT: L 534 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: L 635 GLU cc_start: 0.5607 (mt-10) cc_final: 0.4962 (pt0) outliers start: 80 outliers final: 27 residues processed: 509 average time/residue: 2.1263 time to fit residues: 1239.5029 Evaluate side-chains 515 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 470 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 460 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 613 MET Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 20.0000 chunk 291 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 chunk 388 optimal weight: 5.9990 chunk 411 optimal weight: 8.9990 chunk 203 optimal weight: 0.2980 chunk 368 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN H 479 ASN H 556 GLN I 479 ASN J 479 ASN J 556 GLN K 479 ASN K 556 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34050 Z= 0.154 Angle : 0.487 6.739 46062 Z= 0.251 Chirality : 0.044 0.226 5142 Planarity : 0.004 0.032 6048 Dihedral : 9.842 167.463 4936 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.97 % Allowed : 10.43 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.13), residues: 4290 helix: 0.56 (0.13), residues: 1500 sheet: 1.26 (0.17), residues: 792 loop : 0.11 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.007 0.001 HIS C 104 PHE 0.011 0.001 PHE C 384 TYR 0.009 0.001 TYR C 173 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 548 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 480 time to evaluate : 3.904 Fit side-chains REVERT: A 21 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 29 LYS cc_start: 0.8263 (tppt) cc_final: 0.7911 (mmmt) REVERT: A 171 ASP cc_start: 0.8422 (m-30) cc_final: 0.7927 (t0) REVERT: A 196 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 257 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: A 267 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8165 (mmtp) REVERT: A 317 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8068 (mtt-85) REVERT: A 400 LYS cc_start: 0.8461 (mttt) cc_final: 0.8136 (mtmp) REVERT: B 21 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7012 (mp0) REVERT: B 22 LYS cc_start: 0.7915 (tttt) cc_final: 0.7436 (ttpt) REVERT: B 171 ASP cc_start: 0.8451 (m-30) cc_final: 0.7888 (t0) REVERT: B 190 MET cc_start: 0.9113 (mtp) cc_final: 0.8896 (mtp) REVERT: B 196 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: B 220 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8626 (mtmm) REVERT: B 257 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: B 266 ASP cc_start: 0.8249 (t70) cc_final: 0.7858 (t0) REVERT: B 267 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8237 (mmtp) REVERT: B 289 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8178 (mtp85) REVERT: B 317 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.7829 (mtm180) REVERT: B 400 LYS cc_start: 0.8464 (mttt) cc_final: 0.8164 (mtmp) REVERT: B 452 GLU cc_start: 0.7894 (tt0) cc_final: 0.7599 (pt0) REVERT: C 6 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6498 (pm20) REVERT: C 9 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 21 GLU cc_start: 0.7825 (tp30) cc_final: 0.7326 (mp0) REVERT: C 22 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7730 (ttpt) REVERT: C 49 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: C 171 ASP cc_start: 0.8455 (m-30) cc_final: 0.8071 (t0) REVERT: C 257 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: C 449 LYS cc_start: 0.7840 (tptt) cc_final: 0.7608 (tptm) REVERT: C 453 ARG cc_start: 0.7101 (mpt-90) cc_final: 0.6553 (mtt180) REVERT: C 455 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7099 (tmmm) REVERT: C 456 GLU cc_start: 0.7486 (pt0) cc_final: 0.7277 (pt0) REVERT: C 458 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7511 (tp30) REVERT: C 475 GLU cc_start: 0.8369 (tp30) cc_final: 0.7986 (tp30) REVERT: C 497 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: C 502 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7748 (ttm170) REVERT: D 21 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7050 (mp0) REVERT: D 22 LYS cc_start: 0.8146 (tttm) cc_final: 0.7840 (ttpt) REVERT: D 117 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8257 (ttmm) REVERT: D 215 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (ttmm) REVERT: D 400 LYS cc_start: 0.8400 (mttt) cc_final: 0.8111 (mtmp) REVERT: D 452 GLU cc_start: 0.7921 (tt0) cc_final: 0.7660 (pt0) REVERT: D 453 ARG cc_start: 0.6866 (mtt-85) cc_final: 0.6246 (mtt180) REVERT: D 475 GLU cc_start: 0.8429 (tp30) cc_final: 0.7841 (tp30) REVERT: D 502 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7668 (ttm110) REVERT: E 22 LYS cc_start: 0.8098 (tttt) cc_final: 0.7596 (ttpt) REVERT: E 220 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8610 (mtmm) REVERT: E 400 LYS cc_start: 0.8386 (mttt) cc_final: 0.8091 (mtmp) REVERT: F 6 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6478 (pm20) REVERT: F 9 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7062 (mm-30) REVERT: F 21 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6840 (mp0) REVERT: F 22 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7318 (pptt) REVERT: F 29 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8152 (mmmt) REVERT: F 49 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: F 171 ASP cc_start: 0.8418 (m-30) cc_final: 0.8025 (t0) REVERT: F 266 ASP cc_start: 0.8594 (t0) cc_final: 0.8327 (t0) REVERT: F 400 LYS cc_start: 0.8458 (mttt) cc_final: 0.8139 (mtmp) REVERT: F 453 ARG cc_start: 0.7237 (mmt180) cc_final: 0.6358 (mtt180) REVERT: F 458 GLU cc_start: 0.7569 (tt0) cc_final: 0.7146 (tp30) REVERT: F 502 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7731 (ttm170) REVERT: G 483 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7897 (mmm160) REVERT: G 534 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (mtt90) REVERT: G 630 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5517 (tm-30) REVERT: G 635 GLU cc_start: 0.5658 (mt-10) cc_final: 0.4680 (pt0) REVERT: H 483 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7823 (mmm160) REVERT: H 490 ARG cc_start: 0.8327 (ptp90) cc_final: 0.8103 (ptp-170) REVERT: H 520 ASP cc_start: 0.6906 (p0) cc_final: 0.6675 (p0) REVERT: H 580 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8224 (mmt-90) REVERT: H 630 GLU cc_start: 0.6701 (tt0) cc_final: 0.6472 (tt0) REVERT: H 635 GLU cc_start: 0.5767 (mt-10) cc_final: 0.5321 (pt0) REVERT: I 483 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7571 (mmm160) REVERT: I 520 ASP cc_start: 0.6361 (m-30) cc_final: 0.6033 (m-30) REVERT: I 521 LEU cc_start: 0.8495 (mt) cc_final: 0.8241 (tp) REVERT: I 527 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7610 (p0) REVERT: I 534 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7303 (mtp85) REVERT: I 630 GLU cc_start: 0.6677 (tt0) cc_final: 0.6365 (tt0) REVERT: J 483 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8039 (mmm160) REVERT: J 630 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5530 (tm-30) REVERT: K 483 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7875 (mmm160) REVERT: K 520 ASP cc_start: 0.5898 (m-30) cc_final: 0.5650 (m-30) REVERT: K 534 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7438 (ttm-80) REVERT: K 613 MET cc_start: 0.5146 (mpp) cc_final: 0.2639 (tmt) REVERT: K 630 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5707 (tm-30) REVERT: K 635 GLU cc_start: 0.5704 (mt-10) cc_final: 0.4605 (pt0) REVERT: K 665 GLU cc_start: 0.4924 (mt-10) cc_final: 0.4588 (mm-30) REVERT: L 483 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7638 (mmm160) REVERT: L 520 ASP cc_start: 0.6153 (m-30) cc_final: 0.5804 (m-30) REVERT: L 635 GLU cc_start: 0.5536 (mt-10) cc_final: 0.4890 (pt0) outliers start: 68 outliers final: 26 residues processed: 506 average time/residue: 2.0233 time to fit residues: 1177.1462 Evaluate side-chains 516 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 474 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain G residue 534 ARG Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 527 ASP Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 527 ASP Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 169 optimal weight: 0.0370 chunk 351 optimal weight: 1.9990 chunk 284 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 369 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN H 479 ASN H 556 GLN J 479 ASN K 479 ASN K 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34050 Z= 0.143 Angle : 0.472 7.614 46062 Z= 0.243 Chirality : 0.044 0.222 5142 Planarity : 0.004 0.034 6048 Dihedral : 9.161 151.232 4936 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.26 % Allowed : 10.64 % Favored : 87.10 % 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: 0.72 (0.13), residues: 4290 helix: 0.62 (0.14), residues: 1500 sheet: 1.30 (0.17), residues: 792 loop : 0.15 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.007 0.001 HIS E 104 PHE 0.010 0.001 PHE D 384 TYR 0.008 0.001 TYR C 173 ARG 0.006 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 549 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 471 time to evaluate : 3.768 Fit side-chains REVERT: A 21 GLU cc_start: 0.7676 (mm-30) cc_final: 0.6964 (mp0) REVERT: A 29 LYS cc_start: 0.8264 (tppt) cc_final: 0.7916 (mmmt) REVERT: A 171 ASP cc_start: 0.8371 (m-30) cc_final: 0.7744 (t0) REVERT: A 196 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: A 257 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: A 267 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8186 (mmtp) REVERT: A 317 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8085 (mtt-85) REVERT: A 400 LYS cc_start: 0.8491 (mttt) cc_final: 0.8179 (mtmp) REVERT: A 430 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8248 (pmm) REVERT: B 21 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7039 (mp0) REVERT: B 22 LYS cc_start: 0.7907 (tttt) cc_final: 0.7425 (ttpt) REVERT: B 171 ASP cc_start: 0.8434 (m-30) cc_final: 0.7928 (t0) REVERT: B 196 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: B 220 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8632 (mtmm) REVERT: B 257 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: B 266 ASP cc_start: 0.8236 (t70) cc_final: 0.7934 (t0) REVERT: B 267 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8240 (mmtp) REVERT: B 317 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7927 (mtp85) REVERT: B 400 LYS cc_start: 0.8525 (mttt) cc_final: 0.8232 (mtmp) REVERT: B 452 GLU cc_start: 0.7839 (tt0) cc_final: 0.7553 (pt0) REVERT: B 502 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7658 (ttm110) REVERT: C 6 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6526 (pm20) REVERT: C 9 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7079 (mm-30) REVERT: C 21 GLU cc_start: 0.7835 (tp30) cc_final: 0.7229 (mp0) REVERT: C 22 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7685 (ttpt) REVERT: C 49 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 171 ASP cc_start: 0.8398 (m-30) cc_final: 0.8011 (t0) REVERT: C 257 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: C 453 ARG cc_start: 0.7060 (mpt-90) cc_final: 0.6746 (mtt180) REVERT: C 455 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7550 (tppp) REVERT: C 458 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7475 (tp30) REVERT: C 497 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: C 502 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7757 (ttm170) REVERT: D 21 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7047 (mp0) REVERT: D 22 LYS cc_start: 0.8160 (tttm) cc_final: 0.7860 (ttpt) REVERT: D 400 LYS cc_start: 0.8422 (mttt) cc_final: 0.8141 (mtmp) REVERT: D 453 ARG cc_start: 0.6835 (mtt-85) cc_final: 0.6264 (mtt180) REVERT: D 455 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7673 (tmtp) REVERT: D 475 GLU cc_start: 0.8432 (tp30) cc_final: 0.7743 (tp30) REVERT: D 497 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: D 502 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7675 (ttm110) REVERT: E 10 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: E 22 LYS cc_start: 0.8109 (tttt) cc_final: 0.7606 (ttpt) REVERT: E 220 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8630 (mtmm) REVERT: E 400 LYS cc_start: 0.8411 (mttt) cc_final: 0.8122 (mtmp) REVERT: F 6 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6497 (pm20) REVERT: F 9 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7067 (mm-30) REVERT: F 21 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6881 (mp0) REVERT: F 22 LYS cc_start: 0.7944 (ptmt) cc_final: 0.7299 (pptt) REVERT: F 29 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8149 (mmmt) REVERT: F 49 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: F 171 ASP cc_start: 0.8377 (m-30) cc_final: 0.7991 (t0) REVERT: F 257 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: F 266 ASP cc_start: 0.8624 (t0) cc_final: 0.8364 (t0) REVERT: F 400 LYS cc_start: 0.8493 (mttt) cc_final: 0.8220 (mtmp) REVERT: F 453 ARG cc_start: 0.7236 (mmt180) cc_final: 0.6378 (mtt180) REVERT: F 458 GLU cc_start: 0.7581 (tt0) cc_final: 0.7160 (tp30) REVERT: F 502 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7744 (ttm170) REVERT: G 483 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7910 (mmm160) REVERT: G 534 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7407 (mtt90) REVERT: G 630 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.5520 (tm-30) REVERT: G 635 GLU cc_start: 0.5697 (mt-10) cc_final: 0.4700 (pt0) REVERT: H 483 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7838 (mmm160) REVERT: H 534 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7729 (mtp85) REVERT: H 580 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8193 (mmt-90) REVERT: H 635 GLU cc_start: 0.5742 (mt-10) cc_final: 0.5274 (pt0) REVERT: I 483 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7576 (mmm160) REVERT: I 520 ASP cc_start: 0.6319 (m-30) cc_final: 0.5957 (m-30) REVERT: I 521 LEU cc_start: 0.8527 (mt) cc_final: 0.8313 (tp) REVERT: I 527 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7615 (p0) REVERT: I 534 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7305 (mtp85) REVERT: I 630 GLU cc_start: 0.6650 (tt0) cc_final: 0.6359 (tt0) REVERT: J 483 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.7983 (mmm160) REVERT: J 630 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5515 (tm-30) REVERT: K 483 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7864 (mmm160) REVERT: K 534 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7480 (ttm170) REVERT: K 613 MET cc_start: 0.5089 (mpp) cc_final: 0.2738 (tmt) REVERT: K 630 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5730 (tm-30) REVERT: K 635 GLU cc_start: 0.5671 (mt-10) cc_final: 0.4604 (pt0) REVERT: K 665 GLU cc_start: 0.4854 (mt-10) cc_final: 0.4580 (mm-30) REVERT: L 483 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7626 (mmm160) REVERT: L 635 GLU cc_start: 0.5453 (mt-10) cc_final: 0.4809 (pt0) outliers start: 78 outliers final: 31 residues processed: 502 average time/residue: 2.0133 time to fit residues: 1162.6041 Evaluate side-chains 507 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 457 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 534 ARG Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 527 ASP Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 2.9990 chunk 370 optimal weight: 0.0030 chunk 81 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 412 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN H 479 ASN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34050 Z= 0.185 Angle : 0.495 8.316 46062 Z= 0.255 Chirality : 0.044 0.229 5142 Planarity : 0.004 0.033 6048 Dihedral : 8.846 122.248 4936 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.20 % Allowed : 10.72 % Favored : 87.07 % 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: 0.67 (0.13), residues: 4290 helix: 0.56 (0.13), residues: 1500 sheet: 1.28 (0.17), residues: 792 loop : 0.15 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 544 HIS 0.008 0.001 HIS E 104 PHE 0.011 0.001 PHE D 384 TYR 0.009 0.001 TYR C 173 ARG 0.007 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 541 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 465 time to evaluate : 4.077 Fit side-chains REVERT: A 21 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6944 (mp0) REVERT: A 29 LYS cc_start: 0.8282 (tppt) cc_final: 0.7929 (mmmt) REVERT: A 171 ASP cc_start: 0.8354 (m-30) cc_final: 0.7755 (t0) REVERT: A 196 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: A 257 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: A 267 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8189 (mmtp) REVERT: A 317 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8073 (mtt-85) REVERT: A 400 LYS cc_start: 0.8490 (mttt) cc_final: 0.8167 (mtmp) REVERT: B 21 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7064 (mp0) REVERT: B 22 LYS cc_start: 0.7917 (tttt) cc_final: 0.7435 (ttpt) REVERT: B 49 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: B 171 ASP cc_start: 0.8458 (m-30) cc_final: 0.7982 (t0) REVERT: B 196 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: B 220 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8611 (mtmm) REVERT: B 257 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 267 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8263 (mmtp) REVERT: B 317 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7914 (mtp85) REVERT: B 400 LYS cc_start: 0.8513 (mttt) cc_final: 0.8227 (mtmp) REVERT: B 452 GLU cc_start: 0.7895 (tt0) cc_final: 0.7595 (pt0) REVERT: C 5 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6092 (mp) REVERT: C 6 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6421 (pm20) REVERT: C 9 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6996 (mm-30) REVERT: C 21 GLU cc_start: 0.7845 (tp30) cc_final: 0.7249 (mp0) REVERT: C 22 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7694 (ttpt) REVERT: C 49 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: C 171 ASP cc_start: 0.8414 (m-30) cc_final: 0.8067 (t0) REVERT: C 257 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: C 453 ARG cc_start: 0.7073 (mpt-90) cc_final: 0.6563 (mtt180) REVERT: C 455 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7567 (tppp) REVERT: C 458 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7490 (tp30) REVERT: C 475 GLU cc_start: 0.8343 (tp30) cc_final: 0.7960 (tp30) REVERT: C 497 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: C 502 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7766 (ttm170) REVERT: D 21 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7052 (mp0) REVERT: D 22 LYS cc_start: 0.8161 (tttm) cc_final: 0.7860 (ttpt) REVERT: D 117 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8301 (ttmm) REVERT: D 215 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: D 400 LYS cc_start: 0.8412 (mttt) cc_final: 0.8130 (mtmp) REVERT: D 453 ARG cc_start: 0.6872 (mtt-85) cc_final: 0.6283 (mtt180) REVERT: D 455 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7657 (tmtp) REVERT: D 475 GLU cc_start: 0.8438 (tp30) cc_final: 0.7874 (tp30) REVERT: D 497 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: E 10 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: E 22 LYS cc_start: 0.8096 (tttt) cc_final: 0.7590 (ttpt) REVERT: E 220 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8623 (mtmm) REVERT: E 400 LYS cc_start: 0.8394 (mttt) cc_final: 0.8105 (mtmp) REVERT: F 6 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6468 (pm20) REVERT: F 9 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7001 (mm-30) REVERT: F 21 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6928 (mp0) REVERT: F 22 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7283 (pptt) REVERT: F 29 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8149 (mmmt) REVERT: F 49 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: F 171 ASP cc_start: 0.8382 (m-30) cc_final: 0.8046 (t0) REVERT: F 257 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: F 266 ASP cc_start: 0.8645 (t0) cc_final: 0.8408 (t0) REVERT: F 400 LYS cc_start: 0.8483 (mttt) cc_final: 0.8210 (mtmp) REVERT: F 453 ARG cc_start: 0.7237 (mmt180) cc_final: 0.6369 (mtt180) REVERT: F 458 GLU cc_start: 0.7585 (tt0) cc_final: 0.7158 (tp30) REVERT: F 502 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7740 (ttm170) REVERT: G 483 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7908 (mmm160) REVERT: G 534 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7385 (mtt90) REVERT: G 630 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: G 635 GLU cc_start: 0.5714 (mt-10) cc_final: 0.4730 (pt0) REVERT: H 483 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7841 (mmm160) REVERT: H 534 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7693 (mtp85) REVERT: H 580 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8228 (mmt-90) REVERT: H 599 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4778 (tmmt) REVERT: H 630 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: H 635 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5314 (pt0) REVERT: I 483 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7581 (mmm160) REVERT: I 520 ASP cc_start: 0.6319 (m-30) cc_final: 0.5917 (m-30) REVERT: I 521 LEU cc_start: 0.8565 (mt) cc_final: 0.8353 (tp) REVERT: I 527 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7646 (p0) REVERT: I 534 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7305 (mtp85) REVERT: I 630 GLU cc_start: 0.6689 (tt0) cc_final: 0.6387 (tt0) REVERT: J 483 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8009 (mmm160) REVERT: J 630 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: K 483 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7856 (mmm160) REVERT: K 534 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7497 (ttm-80) REVERT: K 613 MET cc_start: 0.5186 (mpp) cc_final: 0.2713 (tmt) REVERT: K 630 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5689 (tm-30) REVERT: K 635 GLU cc_start: 0.5754 (mt-10) cc_final: 0.4585 (pt0) REVERT: K 665 GLU cc_start: 0.4943 (mt-10) cc_final: 0.4630 (mm-30) REVERT: L 483 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7633 (mmm160) REVERT: L 635 GLU cc_start: 0.5467 (mt-10) cc_final: 0.4813 (pt0) outliers start: 76 outliers final: 34 residues processed: 495 average time/residue: 2.0012 time to fit residues: 1139.3531 Evaluate side-chains 513 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 455 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 534 ARG Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain I residue 482 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 613 MET Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 527 ASP Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 410 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN G 556 GLN H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 34050 Z= 0.442 Angle : 0.612 9.240 46062 Z= 0.320 Chirality : 0.051 0.245 5142 Planarity : 0.005 0.041 6048 Dihedral : 9.025 126.273 4936 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.70 % Allowed : 10.46 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4290 helix: 0.29 (0.13), residues: 1488 sheet: 1.24 (0.17), residues: 792 loop : 0.02 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 537 HIS 0.012 0.002 HIS B 104 PHE 0.016 0.002 PHE D 384 TYR 0.016 0.002 TYR F 173 ARG 0.006 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 557 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 464 time to evaluate : 3.919 Fit side-chains REVERT: A 21 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6972 (mp0) REVERT: A 29 LYS cc_start: 0.8302 (tppt) cc_final: 0.7947 (mmmt) REVERT: A 171 ASP cc_start: 0.8474 (m-30) cc_final: 0.8138 (t0) REVERT: A 257 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 267 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8231 (mmtp) REVERT: A 285 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: A 317 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.7937 (mtp85) REVERT: A 400 LYS cc_start: 0.8593 (mttt) cc_final: 0.8215 (mtmp) REVERT: B 21 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7015 (mp0) REVERT: B 22 LYS cc_start: 0.8012 (tttt) cc_final: 0.7543 (ttpt) REVERT: B 171 ASP cc_start: 0.8542 (m-30) cc_final: 0.8173 (t0) REVERT: B 215 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8418 (tttm) REVERT: B 220 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8607 (mtmt) REVERT: B 257 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: B 267 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8250 (mmtp) REVERT: B 317 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7974 (mtp85) REVERT: B 400 LYS cc_start: 0.8638 (mttt) cc_final: 0.8296 (mttp) REVERT: C 5 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6264 (mp) REVERT: C 6 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6548 (pm20) REVERT: C 9 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 21 GLU cc_start: 0.7853 (tp30) cc_final: 0.7280 (mp0) REVERT: C 22 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7697 (ttpt) REVERT: C 49 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: C 171 ASP cc_start: 0.8481 (m-30) cc_final: 0.8160 (t0) REVERT: C 257 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: C 453 ARG cc_start: 0.7074 (mpt-90) cc_final: 0.6664 (mtt180) REVERT: C 455 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7172 (tmmm) REVERT: C 458 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7484 (tp30) REVERT: C 475 GLU cc_start: 0.8344 (tp30) cc_final: 0.7924 (tp30) REVERT: C 502 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7826 (ttm170) REVERT: D 21 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7030 (mp0) REVERT: D 22 LYS cc_start: 0.8201 (tttm) cc_final: 0.7886 (ttpt) REVERT: D 117 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8274 (ttmm) REVERT: D 196 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: D 215 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8343 (ttmm) REVERT: D 257 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: D 400 LYS cc_start: 0.8486 (mttt) cc_final: 0.8173 (mttp) REVERT: D 453 ARG cc_start: 0.6919 (mtt-85) cc_final: 0.6309 (mtt180) REVERT: D 455 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (tmtp) REVERT: D 475 GLU cc_start: 0.8457 (tp30) cc_final: 0.7858 (tp30) REVERT: D 497 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: E 10 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: E 22 LYS cc_start: 0.8116 (tttt) cc_final: 0.7606 (ttpt) REVERT: E 220 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8669 (mtmm) REVERT: E 257 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: E 400 LYS cc_start: 0.8469 (mttt) cc_final: 0.8152 (mttp) REVERT: F 6 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6527 (pm20) REVERT: F 9 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7016 (mm-30) REVERT: F 21 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6967 (mp0) REVERT: F 22 LYS cc_start: 0.8053 (ptmt) cc_final: 0.7317 (pptt) REVERT: F 29 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8138 (mmmt) REVERT: F 49 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: F 171 ASP cc_start: 0.8432 (m-30) cc_final: 0.8161 (t0) REVERT: F 257 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: F 266 ASP cc_start: 0.8740 (t0) cc_final: 0.8518 (t0) REVERT: F 400 LYS cc_start: 0.8600 (mttt) cc_final: 0.8299 (mttp) REVERT: F 453 ARG cc_start: 0.7200 (mmt180) cc_final: 0.6349 (mtt180) REVERT: F 458 GLU cc_start: 0.7638 (tt0) cc_final: 0.7209 (tp30) REVERT: F 502 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7815 (ttm170) REVERT: G 483 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7929 (mmm160) REVERT: G 534 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7569 (mtp180) REVERT: G 630 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5511 (tm-30) REVERT: G 635 GLU cc_start: 0.5778 (mt-10) cc_final: 0.4707 (pt0) REVERT: H 483 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7851 (mmm160) REVERT: H 580 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8218 (mmt-90) REVERT: H 630 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: H 635 GLU cc_start: 0.5880 (mt-10) cc_final: 0.5192 (pt0) REVERT: I 483 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7582 (mmm160) REVERT: I 520 ASP cc_start: 0.6453 (m-30) cc_final: 0.6077 (m-30) REVERT: I 527 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7735 (p0) REVERT: I 534 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7320 (mtp85) REVERT: I 630 GLU cc_start: 0.6854 (tt0) cc_final: 0.6527 (tt0) REVERT: J 483 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8053 (mmm160) REVERT: J 630 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5553 (tm-30) REVERT: K 483 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7853 (mmm160) REVERT: K 534 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7587 (ttm-80) REVERT: K 613 MET cc_start: 0.5126 (mpp) cc_final: 0.2660 (tmt) REVERT: K 630 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5599 (tm-30) REVERT: K 635 GLU cc_start: 0.5801 (mt-10) cc_final: 0.4635 (pt0) REVERT: K 665 GLU cc_start: 0.4986 (mt-10) cc_final: 0.4664 (mm-30) REVERT: L 483 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7611 (mmm160) REVERT: L 635 GLU cc_start: 0.5483 (mt-10) cc_final: 0.4748 (pt0) outliers start: 93 outliers final: 38 residues processed: 499 average time/residue: 1.9980 time to fit residues: 1149.3221 Evaluate side-chains 520 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 458 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 460 GLU Chi-restraints excluded: chain G residue 534 ARG Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 594 ASN Chi-restraints excluded: chain I residue 613 MET Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 527 ASP Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 245 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 203 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN H 479 ASN J 479 ASN J 556 GLN K 479 ASN K 556 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34050 Z= 0.148 Angle : 0.481 9.147 46062 Z= 0.248 Chirality : 0.044 0.191 5142 Planarity : 0.004 0.035 6048 Dihedral : 8.360 132.753 4936 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.71 % Allowed : 11.71 % Favored : 86.58 % 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: 0.59 (0.13), residues: 4290 helix: 0.50 (0.13), residues: 1500 sheet: 1.24 (0.17), residues: 792 loop : 0.09 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 544 HIS 0.007 0.001 HIS E 104 PHE 0.011 0.001 PHE B 384 TYR 0.010 0.001 TYR F 173 ARG 0.011 0.000 ARG H 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 521 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 462 time to evaluate : 3.967 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6975 (mp0) REVERT: A 29 LYS cc_start: 0.8291 (tppt) cc_final: 0.7936 (mmmt) REVERT: A 171 ASP cc_start: 0.8341 (m-30) cc_final: 0.7812 (t0) REVERT: A 196 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: A 215 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (tttm) REVERT: A 257 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: A 267 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8181 (mmtp) REVERT: A 317 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8077 (mtt-85) REVERT: A 400 LYS cc_start: 0.8495 (mttt) cc_final: 0.8152 (mtmp) REVERT: B 21 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7045 (mp0) REVERT: B 22 LYS cc_start: 0.7909 (tttt) cc_final: 0.7431 (ttpt) REVERT: B 171 ASP cc_start: 0.8420 (m-30) cc_final: 0.7975 (t0) REVERT: B 196 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: B 220 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8608 (mtmm) REVERT: B 267 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8255 (mmtp) REVERT: B 317 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7926 (mtp85) REVERT: B 400 LYS cc_start: 0.8495 (mttt) cc_final: 0.8186 (mtmp) REVERT: C 6 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6410 (pm20) REVERT: C 9 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6999 (mm-30) REVERT: C 21 GLU cc_start: 0.7794 (tp30) cc_final: 0.7260 (mp0) REVERT: C 22 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7738 (ttpt) REVERT: C 49 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: C 171 ASP cc_start: 0.8397 (m-30) cc_final: 0.8041 (t0) REVERT: C 257 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 453 ARG cc_start: 0.7031 (mpt-90) cc_final: 0.6616 (mtt180) REVERT: C 455 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7596 (tppp) REVERT: C 458 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7501 (tp30) REVERT: C 475 GLU cc_start: 0.8353 (tp30) cc_final: 0.7983 (tp30) REVERT: C 497 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: C 502 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7752 (ttm170) REVERT: D 21 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7117 (mp0) REVERT: D 22 LYS cc_start: 0.8185 (tttm) cc_final: 0.7879 (ttpt) REVERT: D 117 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8238 (ttmm) REVERT: D 215 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8155 (ttmm) REVERT: D 400 LYS cc_start: 0.8429 (mttt) cc_final: 0.8106 (mtmp) REVERT: D 452 GLU cc_start: 0.7954 (tt0) cc_final: 0.7611 (pt0) REVERT: D 453 ARG cc_start: 0.6896 (mtt-85) cc_final: 0.6305 (mtt180) REVERT: D 455 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7606 (tmtp) REVERT: D 475 GLU cc_start: 0.8418 (tp30) cc_final: 0.7824 (tp30) REVERT: E 10 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: E 22 LYS cc_start: 0.8098 (tttt) cc_final: 0.7590 (ttpt) REVERT: E 220 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8625 (mtmm) REVERT: E 400 LYS cc_start: 0.8410 (mttt) cc_final: 0.8082 (mtmp) REVERT: F 6 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6476 (pm20) REVERT: F 9 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7084 (mm-30) REVERT: F 21 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6927 (mp0) REVERT: F 22 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7336 (pptt) REVERT: F 29 LYS cc_start: 0.8368 (mmtp) cc_final: 0.8132 (mmmt) REVERT: F 49 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: F 171 ASP cc_start: 0.8367 (m-30) cc_final: 0.8030 (t0) REVERT: F 266 ASP cc_start: 0.8612 (t0) cc_final: 0.8339 (t0) REVERT: F 400 LYS cc_start: 0.8464 (mttt) cc_final: 0.8188 (mtmp) REVERT: F 453 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6349 (mtt180) REVERT: F 458 GLU cc_start: 0.7631 (tt0) cc_final: 0.7196 (tp30) REVERT: F 502 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7734 (ttm170) REVERT: G 483 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7909 (mmm160) REVERT: G 630 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5494 (tm-30) REVERT: G 635 GLU cc_start: 0.5614 (mt-10) cc_final: 0.4650 (pt0) REVERT: H 483 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7824 (mmm160) REVERT: H 534 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7735 (mtp85) REVERT: H 580 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.8209 (mmt-90) REVERT: H 599 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4786 (tmmt) REVERT: H 630 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: H 635 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5203 (pt0) REVERT: I 483 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7545 (mmm160) REVERT: I 520 ASP cc_start: 0.6301 (m-30) cc_final: 0.5903 (m-30) REVERT: I 521 LEU cc_start: 0.8460 (mt) cc_final: 0.8241 (tp) REVERT: I 527 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7697 (p0) REVERT: I 534 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7274 (mtp85) REVERT: I 630 GLU cc_start: 0.6708 (tt0) cc_final: 0.6395 (tt0) REVERT: J 483 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.7999 (mmm160) REVERT: J 630 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.5483 (tm-30) REVERT: K 483 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7850 (mmm160) REVERT: K 534 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7516 (ttm-80) REVERT: K 613 MET cc_start: 0.5089 (mpp) cc_final: 0.2697 (tmt) REVERT: K 630 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5631 (tm-30) REVERT: K 635 GLU cc_start: 0.5722 (mt-10) cc_final: 0.4633 (pt0) REVERT: L 483 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7615 (mmm160) REVERT: L 635 GLU cc_start: 0.5453 (mt-10) cc_final: 0.4737 (pt0) outliers start: 59 outliers final: 29 residues processed: 489 average time/residue: 2.0290 time to fit residues: 1141.7168 Evaluate side-chains 510 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 462 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 594 ASN Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 6.9990 chunk 393 optimal weight: 0.8980 chunk 358 optimal weight: 5.9990 chunk 382 optimal weight: 20.0000 chunk 230 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 381 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN ** G 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 34050 Z= 0.371 Angle : 0.580 9.902 46062 Z= 0.303 Chirality : 0.049 0.218 5142 Planarity : 0.005 0.035 6048 Dihedral : 8.431 127.580 4936 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 11.62 % Favored : 86.58 % 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: 0.46 (0.13), residues: 4290 helix: 0.34 (0.13), residues: 1488 sheet: 1.24 (0.17), residues: 792 loop : 0.02 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 537 HIS 0.012 0.002 HIS B 104 PHE 0.017 0.002 PHE D 384 TYR 0.015 0.002 TYR F 173 ARG 0.008 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 532 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 470 time to evaluate : 3.939 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6972 (mp0) REVERT: A 29 LYS cc_start: 0.8289 (tppt) cc_final: 0.7932 (mmmt) REVERT: A 171 ASP cc_start: 0.8423 (m-30) cc_final: 0.8124 (t0) REVERT: A 196 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: A 215 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8313 (tttm) REVERT: A 257 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 267 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8222 (mmtp) REVERT: A 317 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.7947 (mtp85) REVERT: A 400 LYS cc_start: 0.8579 (mttt) cc_final: 0.8226 (mtmp) REVERT: B 21 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7050 (mp0) REVERT: B 22 LYS cc_start: 0.8004 (tttt) cc_final: 0.7536 (ttpt) REVERT: B 171 ASP cc_start: 0.8514 (m-30) cc_final: 0.8133 (t0) REVERT: B 196 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: B 215 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: B 220 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8604 (mtmt) REVERT: B 257 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 267 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8248 (mmtp) REVERT: B 317 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.7811 (mtm180) REVERT: B 400 LYS cc_start: 0.8615 (mttt) cc_final: 0.8290 (mtmp) REVERT: B 430 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8050 (pmm) REVERT: C 6 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6484 (pm20) REVERT: C 9 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7030 (mm-30) REVERT: C 21 GLU cc_start: 0.7849 (tp30) cc_final: 0.7283 (mp0) REVERT: C 22 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7683 (ttpt) REVERT: C 49 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: C 171 ASP cc_start: 0.8428 (m-30) cc_final: 0.8110 (t0) REVERT: C 257 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 453 ARG cc_start: 0.7056 (mpt-90) cc_final: 0.6619 (mtt180) REVERT: C 455 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7164 (tmmm) REVERT: C 458 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7480 (tp30) REVERT: C 475 GLU cc_start: 0.8341 (tp30) cc_final: 0.7924 (tp30) REVERT: C 497 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: C 502 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7814 (ttm170) REVERT: D 21 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7100 (mp0) REVERT: D 22 LYS cc_start: 0.8201 (tttm) cc_final: 0.7887 (ttpt) REVERT: D 117 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8278 (ttmm) REVERT: D 215 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8325 (ttmm) REVERT: D 400 LYS cc_start: 0.8477 (mttt) cc_final: 0.8175 (mttp) REVERT: D 452 GLU cc_start: 0.7962 (tt0) cc_final: 0.7641 (pt0) REVERT: D 453 ARG cc_start: 0.6915 (mtt-85) cc_final: 0.6288 (mtt180) REVERT: D 455 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7666 (tmtp) REVERT: D 475 GLU cc_start: 0.8455 (tp30) cc_final: 0.7856 (tp30) REVERT: D 497 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: E 10 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: E 22 LYS cc_start: 0.8116 (tttt) cc_final: 0.7606 (ttpt) REVERT: E 220 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8658 (mtmm) REVERT: E 400 LYS cc_start: 0.8461 (mttt) cc_final: 0.8153 (mttp) REVERT: F 6 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6513 (pm20) REVERT: F 9 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7018 (mm-30) REVERT: F 21 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6964 (mp0) REVERT: F 22 LYS cc_start: 0.8040 (ptmt) cc_final: 0.7304 (pptt) REVERT: F 29 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8122 (mmmt) REVERT: F 49 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: F 171 ASP cc_start: 0.8399 (m-30) cc_final: 0.8117 (t0) REVERT: F 257 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: F 266 ASP cc_start: 0.8720 (t0) cc_final: 0.8496 (t0) REVERT: F 400 LYS cc_start: 0.8576 (mttt) cc_final: 0.8294 (mtmp) REVERT: F 453 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6346 (mtt180) REVERT: F 458 GLU cc_start: 0.7647 (tt0) cc_final: 0.7216 (tp30) REVERT: F 502 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7815 (ttm170) REVERT: G 483 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7936 (mmm160) REVERT: G 630 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: G 635 GLU cc_start: 0.5720 (mt-10) cc_final: 0.4666 (pt0) REVERT: H 483 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7814 (mmm160) REVERT: H 534 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7756 (mtp85) REVERT: H 580 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8225 (mmt-90) REVERT: H 630 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: H 635 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5188 (pt0) REVERT: I 483 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7578 (mmm160) REVERT: I 520 ASP cc_start: 0.6410 (m-30) cc_final: 0.6091 (m-30) REVERT: I 521 LEU cc_start: 0.8555 (mt) cc_final: 0.8273 (tp) REVERT: I 527 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7751 (p0) REVERT: I 534 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7329 (mtp85) REVERT: I 630 GLU cc_start: 0.6847 (tt0) cc_final: 0.6516 (tt0) REVERT: J 483 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.8042 (mmm160) REVERT: J 630 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.5474 (tm-30) REVERT: K 483 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7851 (mmm160) REVERT: K 534 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7572 (ttm-80) REVERT: K 630 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5584 (tm-30) REVERT: K 635 GLU cc_start: 0.5739 (mt-10) cc_final: 0.4636 (pt0) REVERT: L 483 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7606 (mmm160) REVERT: L 635 GLU cc_start: 0.5527 (mt-10) cc_final: 0.4717 (pt0) outliers start: 62 outliers final: 34 residues processed: 498 average time/residue: 1.9797 time to fit residues: 1136.4254 Evaluate side-chains 514 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 457 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 594 ASN Chi-restraints excluded: chain I residue 613 MET Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 0.9990 chunk 404 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 424 optimal weight: 20.0000 chunk 390 optimal weight: 0.0870 chunk 337 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN G 479 ASN G 556 GLN H 479 ASN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34050 Z= 0.155 Angle : 0.485 9.679 46062 Z= 0.251 Chirality : 0.044 0.187 5142 Planarity : 0.004 0.035 6048 Dihedral : 7.980 116.231 4936 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.54 % Allowed : 12.09 % Favored : 86.38 % 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: 0.56 (0.13), residues: 4290 helix: 0.47 (0.13), residues: 1500 sheet: 1.23 (0.17), residues: 792 loop : 0.08 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 544 HIS 0.007 0.001 HIS E 104 PHE 0.010 0.001 PHE B 384 TYR 0.010 0.001 TYR C 173 ARG 0.007 0.000 ARG A 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 510 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 457 time to evaluate : 3.840 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6975 (mp0) REVERT: A 29 LYS cc_start: 0.8295 (tppt) cc_final: 0.7943 (mmmt) REVERT: A 171 ASP cc_start: 0.8354 (m-30) cc_final: 0.7838 (t0) REVERT: A 196 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: A 215 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8179 (tttm) REVERT: A 257 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: A 267 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8199 (mmtp) REVERT: A 317 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8071 (mtt-85) REVERT: A 400 LYS cc_start: 0.8493 (mttt) cc_final: 0.8154 (mtmp) REVERT: B 21 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7015 (mp0) REVERT: B 22 LYS cc_start: 0.7910 (tttt) cc_final: 0.7433 (ttpt) REVERT: B 171 ASP cc_start: 0.8434 (m-30) cc_final: 0.7996 (t0) REVERT: B 196 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 220 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8608 (mtmm) REVERT: B 267 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8255 (mmtp) REVERT: B 317 ARG cc_start: 0.8399 (mtt-85) cc_final: 0.7926 (mtp85) REVERT: B 400 LYS cc_start: 0.8515 (mttt) cc_final: 0.8211 (mtmp) REVERT: B 430 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7681 (pmm) REVERT: C 6 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6397 (pm20) REVERT: C 9 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7002 (mm-30) REVERT: C 21 GLU cc_start: 0.7837 (tp30) cc_final: 0.7320 (mp0) REVERT: C 22 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7738 (ttpt) REVERT: C 49 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: C 171 ASP cc_start: 0.8399 (m-30) cc_final: 0.8047 (t0) REVERT: C 257 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: C 453 ARG cc_start: 0.7033 (mpt-90) cc_final: 0.6607 (mtt180) REVERT: C 455 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7601 (tppp) REVERT: C 458 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7448 (tp30) REVERT: C 475 GLU cc_start: 0.8324 (tp30) cc_final: 0.7955 (tp30) REVERT: C 497 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: C 502 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7752 (ttm170) REVERT: D 21 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7106 (mp0) REVERT: D 22 LYS cc_start: 0.8190 (tttm) cc_final: 0.7883 (ttpt) REVERT: D 117 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8243 (ttmm) REVERT: D 215 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8175 (ttmm) REVERT: D 400 LYS cc_start: 0.8435 (mttt) cc_final: 0.8117 (mtmp) REVERT: D 452 GLU cc_start: 0.7954 (tt0) cc_final: 0.7644 (pt0) REVERT: D 453 ARG cc_start: 0.6947 (mtt-85) cc_final: 0.6333 (mtt180) REVERT: D 455 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7602 (tmtp) REVERT: D 475 GLU cc_start: 0.8421 (tp30) cc_final: 0.7824 (tp30) REVERT: E 10 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: E 22 LYS cc_start: 0.8097 (tttt) cc_final: 0.7585 (ttpt) REVERT: E 220 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8633 (mtmm) REVERT: E 257 GLU cc_start: 0.7743 (tt0) cc_final: 0.7507 (tm-30) REVERT: E 400 LYS cc_start: 0.8414 (mttt) cc_final: 0.8091 (mtmp) REVERT: F 6 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6419 (pm20) REVERT: F 9 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7087 (mm-30) REVERT: F 21 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6965 (mp0) REVERT: F 22 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7337 (pptt) REVERT: F 29 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8120 (mmmt) REVERT: F 49 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: F 171 ASP cc_start: 0.8345 (m-30) cc_final: 0.8029 (t0) REVERT: F 266 ASP cc_start: 0.8617 (t0) cc_final: 0.8359 (t0) REVERT: F 400 LYS cc_start: 0.8487 (mttt) cc_final: 0.8216 (mtmp) REVERT: F 453 ARG cc_start: 0.7205 (mmt180) cc_final: 0.6328 (mtt180) REVERT: F 458 GLU cc_start: 0.7637 (tt0) cc_final: 0.7202 (tp30) REVERT: F 502 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7737 (ttm170) REVERT: G 483 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7911 (mmm160) REVERT: G 630 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: G 635 GLU cc_start: 0.5625 (mt-10) cc_final: 0.4622 (pt0) REVERT: H 483 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7823 (mmm160) REVERT: H 534 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7656 (mtp85) REVERT: H 580 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.8213 (mmt-90) REVERT: H 599 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4787 (tmmt) REVERT: H 630 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: H 635 GLU cc_start: 0.5751 (mt-10) cc_final: 0.5202 (pt0) REVERT: I 483 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7547 (mmm160) REVERT: I 520 ASP cc_start: 0.6431 (m-30) cc_final: 0.5983 (m-30) REVERT: I 521 LEU cc_start: 0.8514 (mt) cc_final: 0.8270 (tp) REVERT: I 527 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7719 (p0) REVERT: I 534 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7275 (mtp85) REVERT: I 630 GLU cc_start: 0.6836 (tt0) cc_final: 0.6548 (tt0) REVERT: J 483 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.7994 (mmm160) REVERT: J 630 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5460 (tm-30) REVERT: K 483 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7852 (mmm160) REVERT: K 534 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7561 (ttm-80) REVERT: K 630 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5608 (tm-30) REVERT: K 635 GLU cc_start: 0.5708 (mt-10) cc_final: 0.4654 (pt0) REVERT: L 483 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7625 (mmm160) REVERT: L 520 ASP cc_start: 0.6348 (m-30) cc_final: 0.6146 (m-30) REVERT: L 635 GLU cc_start: 0.5510 (mt-10) cc_final: 0.4725 (pt0) outliers start: 53 outliers final: 31 residues processed: 481 average time/residue: 2.0036 time to fit residues: 1112.8543 Evaluate side-chains 506 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 455 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 527 ASP Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain I residue 594 ASN Chi-restraints excluded: chain I residue 613 MET Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.3980 chunk 360 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 311 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN G 479 ASN ** G 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.082443 restraints weight = 33999.907| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.84 r_work: 0.2829 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34050 Z= 0.243 Angle : 0.522 10.051 46062 Z= 0.271 Chirality : 0.046 0.194 5142 Planarity : 0.004 0.035 6048 Dihedral : 8.024 122.127 4936 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.65 % Allowed : 11.94 % Favored : 86.41 % 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: 0.56 (0.13), residues: 4290 helix: 0.47 (0.13), residues: 1482 sheet: 1.25 (0.17), residues: 792 loop : 0.06 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 544 HIS 0.009 0.001 HIS E 104 PHE 0.013 0.001 PHE E 384 TYR 0.011 0.002 TYR C 173 ARG 0.007 0.000 ARG A 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17239.80 seconds wall clock time: 307 minutes 57.67 seconds (18477.67 seconds total)