Starting phenix.real_space_refine on Sun Apr 14 21:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dck_27326/04_2024/8dck_27326_updated.pdb" } resolution = 3.4 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= 0.111 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 21126 2.51 5 N 5610 2.21 5 O 5823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32661 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "I" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.59, per 1000 atoms: 0.51 Number of scatterers: 32661 At special positions: 0 Unit cell: (144.3, 152.1, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 18 15.00 Mg 6 11.99 O 5823 8.00 N 5610 7.00 C 21126 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=0, symmetry=0 Time building additional restraints: 14.31 Conformation dependent library (CDL) restraints added in 5.7 seconds 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 18 sheets defined 59.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 140 through 149 Proline residue: A 145 - end of helix removed outlier: 3.755A pdb=" N LYS A 149 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 180 Proline residue: A 172 - end of helix removed outlier: 3.831A pdb=" N PHE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 236 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.856A pdb=" N LEU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.657A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 295 through 338 Proline residue: A 302 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 349 through 402 removed outlier: 3.621A pdb=" N LEU A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 429 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.851A pdb=" N THR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 641 through 651 removed outlier: 4.836A pdb=" N HIS A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'B' and resid 141 through 149 Proline residue: B 145 - end of helix Processing helix chain 'B' and resid 151 through 178 removed outlier: 3.870A pdb=" N PHE B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Proline residue: B 172 - end of helix Processing helix chain 'B' and resid 189 through 236 removed outlier: 3.619A pdb=" N VAL B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 222 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.813A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 289 removed outlier: 4.533A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 338 Proline residue: B 302 - end of helix Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 350 through 402 Processing helix chain 'B' and resid 407 through 448 Proline residue: B 423 - end of helix removed outlier: 4.001A pdb=" N ILE B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.705A pdb=" N THR B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 638 through 651 removed outlier: 4.465A pdb=" N HIS B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'D' and resid 10 through 25 removed outlier: 4.223A pdb=" N ILE D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 39 No H-bonds generated for 'chain 'D' and resid 36 through 39' Processing helix chain 'D' and resid 44 through 50 Processing helix chain 'D' and resid 56 through 76 Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 27 through 34 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 66 through 68 No H-bonds generated for 'chain 'I' and resid 66 through 68' Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 140 through 149 Proline residue: I 145 - end of helix removed outlier: 3.755A pdb=" N LYS I 149 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 180 Proline residue: I 172 - end of helix removed outlier: 3.831A pdb=" N PHE I 175 " --> pdb=" O THR I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 236 Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.856A pdb=" N LEU I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 277 Processing helix chain 'I' and resid 280 through 289 removed outlier: 3.657A pdb=" N VAL I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 295 through 338 Proline residue: I 302 - end of helix Proline residue: I 313 - end of helix Processing helix chain 'I' and resid 340 through 345 Processing helix chain 'I' and resid 349 through 402 removed outlier: 3.621A pdb=" N LEU I 373 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 429 Proline residue: I 423 - end of helix Processing helix chain 'I' and resid 431 through 448 removed outlier: 3.851A pdb=" N THR I 442 " --> pdb=" O GLY I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 515 Processing helix chain 'I' and resid 538 through 544 Processing helix chain 'I' and resid 559 through 565 Processing helix chain 'I' and resid 573 through 582 Processing helix chain 'I' and resid 585 through 589 Processing helix chain 'I' and resid 594 through 596 No H-bonds generated for 'chain 'I' and resid 594 through 596' Processing helix chain 'I' and resid 601 through 603 No H-bonds generated for 'chain 'I' and resid 601 through 603' Processing helix chain 'I' and resid 608 through 620 Processing helix chain 'I' and resid 641 through 651 removed outlier: 4.836A pdb=" N HIS I 649 " --> pdb=" O MET I 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS I 650 " --> pdb=" O ARG I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' Processing helix chain 'I' and resid 687 through 691 Processing helix chain 'I' and resid 697 through 701 Processing helix chain 'J' and resid 141 through 149 Proline residue: J 145 - end of helix Processing helix chain 'J' and resid 151 through 178 removed outlier: 3.870A pdb=" N PHE J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Proline residue: J 172 - end of helix Processing helix chain 'J' and resid 189 through 236 removed outlier: 3.619A pdb=" N VAL J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG J 222 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 244 Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.813A pdb=" N LEU J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 289 removed outlier: 4.533A pdb=" N PHE J 280 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE J 281 " --> pdb=" O LEU J 277 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE J 282 " --> pdb=" O PHE J 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE J 283 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA J 284 " --> pdb=" O PHE J 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 338 Proline residue: J 302 - end of helix Proline residue: J 313 - end of helix Processing helix chain 'J' and resid 340 through 345 Processing helix chain 'J' and resid 350 through 402 Processing helix chain 'J' and resid 407 through 448 Proline residue: J 423 - end of helix removed outlier: 4.001A pdb=" N ILE J 430 " --> pdb=" O ARG J 426 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN J 432 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP J 433 " --> pdb=" O GLN J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 515 removed outlier: 3.705A pdb=" N THR J 512 " --> pdb=" O LYS J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 544 Processing helix chain 'J' and resid 559 through 563 Processing helix chain 'J' and resid 572 through 581 Processing helix chain 'J' and resid 585 through 590 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 608 through 620 Processing helix chain 'J' and resid 638 through 651 removed outlier: 4.465A pdb=" N HIS J 649 " --> pdb=" O MET J 645 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS J 650 " --> pdb=" O ARG J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 687 through 691 Processing helix chain 'J' and resid 697 through 705 Processing helix chain 'K' and resid 35 through 38 No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 43 through 48 Processing helix chain 'K' and resid 59 through 64 Processing helix chain 'L' and resid 10 through 25 removed outlier: 4.222A pdb=" N ILE L 25 " --> pdb=" O GLU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 39 No H-bonds generated for 'chain 'L' and resid 36 through 39' Processing helix chain 'L' and resid 44 through 50 Processing helix chain 'L' and resid 56 through 76 Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 43 through 52 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 140 through 149 Proline residue: E 145 - end of helix removed outlier: 3.755A pdb=" N LYS E 149 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 180 Proline residue: E 172 - end of helix removed outlier: 3.831A pdb=" N PHE E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 236 Processing helix chain 'E' and resid 240 through 245 Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.856A pdb=" N LEU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.657A pdb=" N VAL E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 295 through 338 Proline residue: E 302 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 340 through 345 Processing helix chain 'E' and resid 349 through 402 removed outlier: 3.621A pdb=" N LEU E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 429 Proline residue: E 423 - end of helix Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.851A pdb=" N THR E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 515 Processing helix chain 'E' and resid 538 through 544 Processing helix chain 'E' and resid 559 through 565 Processing helix chain 'E' and resid 573 through 582 Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 594 through 596 No H-bonds generated for 'chain 'E' and resid 594 through 596' Processing helix chain 'E' and resid 601 through 603 No H-bonds generated for 'chain 'E' and resid 601 through 603' Processing helix chain 'E' and resid 608 through 620 Processing helix chain 'E' and resid 641 through 651 removed outlier: 4.836A pdb=" N HIS E 649 " --> pdb=" O MET E 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 666 No H-bonds generated for 'chain 'E' and resid 664 through 666' Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 697 through 701 Processing helix chain 'F' and resid 141 through 149 Proline residue: F 145 - end of helix Processing helix chain 'F' and resid 151 through 178 removed outlier: 3.870A pdb=" N PHE F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Proline residue: F 172 - end of helix Processing helix chain 'F' and resid 189 through 236 removed outlier: 3.619A pdb=" N VAL F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG F 222 " --> pdb=" O HIS F 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.814A pdb=" N LEU F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 289 removed outlier: 4.533A pdb=" N PHE F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 284 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 338 Proline residue: F 302 - end of helix Proline residue: F 313 - end of helix Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 350 through 402 Processing helix chain 'F' and resid 407 through 448 Proline residue: F 423 - end of helix removed outlier: 4.001A pdb=" N ILE F 430 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASP F 433 " --> pdb=" O GLN F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 515 removed outlier: 3.705A pdb=" N THR F 512 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 544 Processing helix chain 'F' and resid 559 through 563 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 585 through 590 Processing helix chain 'F' and resid 594 through 596 No H-bonds generated for 'chain 'F' and resid 594 through 596' Processing helix chain 'F' and resid 608 through 620 Processing helix chain 'F' and resid 638 through 651 removed outlier: 4.465A pdb=" N HIS F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 697 through 705 Processing helix chain 'G' and resid 35 through 38 No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'H' and resid 10 through 25 removed outlier: 4.223A pdb=" N ILE H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 39 No H-bonds generated for 'chain 'H' and resid 36 through 39' Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 56 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 Processing sheet with id= B, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.818A pdb=" N PHE A 84 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 97 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 89 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG A 95 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 490 through 492 Processing sheet with id= D, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.708A pdb=" N VAL A 675 " --> pdb=" O VAL A 682 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 468 through 471 Processing sheet with id= F, first strand: chain 'B' and resid 680 through 685 removed outlier: 6.821A pdb=" N VAL B 675 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN B 684 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 673 " --> pdb=" O GLN B 684 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 56 through 61 Processing sheet with id= H, first strand: chain 'I' and resid 74 through 76 removed outlier: 3.819A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU I 97 " --> pdb=" O THR I 87 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL I 89 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG I 95 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 490 through 492 Processing sheet with id= J, first strand: chain 'I' and resid 680 through 683 removed outlier: 6.708A pdb=" N VAL I 675 " --> pdb=" O VAL I 682 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 468 through 471 Processing sheet with id= L, first strand: chain 'J' and resid 680 through 685 removed outlier: 6.821A pdb=" N VAL J 675 " --> pdb=" O VAL J 682 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN J 684 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE J 673 " --> pdb=" O GLN J 684 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 56 through 61 Processing sheet with id= N, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.819A pdb=" N PHE E 84 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 97 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 89 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG E 95 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 490 through 492 Processing sheet with id= P, first strand: chain 'E' and resid 680 through 683 removed outlier: 6.708A pdb=" N VAL E 675 " --> pdb=" O VAL E 682 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 468 through 471 Processing sheet with id= R, first strand: chain 'F' and resid 680 through 685 removed outlier: 6.821A pdb=" N VAL F 675 " --> pdb=" O VAL F 682 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 684 " --> pdb=" O ILE F 673 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 673 " --> pdb=" O GLN F 684 " (cutoff:3.500A) 1806 hydrogen bonds defined for protein. 5265 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: 11.89 Time building geometry restraints manager: 15.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7427 1.33 - 1.45: 6756 1.45 - 1.57: 18937 1.57 - 1.70: 33 1.70 - 1.82: 144 Bond restraints: 33297 Sorted by residual: bond pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 1.531 1.492 0.040 1.32e-02 5.74e+03 8.97e+00 bond pdb=" CA ARG I 246 " pdb=" C ARG I 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.93e+00 bond pdb=" CA ARG E 246 " pdb=" C ARG E 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.87e+00 bond pdb=" CA TYR A 9 " pdb=" C TYR A 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" CA TYR I 9 " pdb=" C TYR I 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.78e+00 ... (remaining 33292 not shown) Histogram of bond angle deviations from ideal: 97.93 - 106.32: 753 106.32 - 114.71: 20411 114.71 - 123.10: 22597 123.10 - 131.49: 1365 131.49 - 139.88: 78 Bond angle restraints: 45204 Sorted by residual: angle pdb=" CA GLU I 573 " pdb=" CB GLU I 573 " pdb=" CG GLU I 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU A 573 " pdb=" CB GLU A 573 " pdb=" CG GLU A 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU E 573 " pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " ideal model delta sigma weight residual 114.10 125.88 -11.78 2.00e+00 2.50e-01 3.47e+01 angle pdb=" C LEU L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.92 114.25 5.67 1.07e+00 8.73e-01 2.81e+01 angle pdb=" C LEU H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.92 114.27 5.65 1.07e+00 8.73e-01 2.79e+01 ... (remaining 45199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 17924 17.45 - 34.89: 1662 34.89 - 52.34: 344 52.34 - 69.79: 74 69.79 - 87.23: 39 Dihedral angle restraints: 20043 sinusoidal: 8118 harmonic: 11925 Sorted by residual: dihedral pdb=" CA PHE A 264 " pdb=" C PHE A 264 " pdb=" N LEU A 265 " pdb=" CA LEU A 265 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE E 264 " pdb=" C PHE E 264 " pdb=" N LEU E 265 " pdb=" CA LEU E 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE I 264 " pdb=" C PHE I 264 " pdb=" N LEU I 265 " pdb=" CA LEU I 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4018 0.049 - 0.098: 1038 0.098 - 0.148: 266 0.148 - 0.197: 6 0.197 - 0.246: 6 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA VAL B 526 " pdb=" N VAL B 526 " pdb=" C VAL B 526 " pdb=" CB VAL B 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL J 526 " pdb=" N VAL J 526 " pdb=" C VAL J 526 " pdb=" CB VAL J 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL F 526 " pdb=" N VAL F 526 " pdb=" C VAL F 526 " pdb=" CB VAL F 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5331 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 245 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER E 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG E 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 245 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER I 245 " 0.042 2.00e-02 2.50e+03 pdb=" O SER I 245 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG I 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 245 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C SER A 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 246 " 0.014 2.00e-02 2.50e+03 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 252 2.59 - 3.17: 27528 3.17 - 3.74: 53244 3.74 - 4.32: 68931 4.32 - 4.90: 114217 Nonbonded interactions: 264172 Sorted by model distance: nonbonded pdb=" OE1 GLN J 550 " pdb="MG MG J 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN B 550 " pdb="MG MG B 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN F 550 " pdb="MG MG F 802 " model vdw 2.013 2.170 nonbonded pdb=" O2B ATP F 801 " pdb="MG MG F 802 " model vdw 2.031 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 2.031 2.170 ... (remaining 264167 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.580 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 86.190 Find NCS groups from input model: 2.330 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.004 0.056 33297 Z= 0.234 Angle : 0.743 15.632 45204 Z= 0.415 Chirality : 0.045 0.246 5334 Planarity : 0.004 0.055 5640 Dihedral : 14.840 87.232 12315 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.17 (0.13), residues: 4071 helix: 0.82 (0.10), residues: 2541 sheet: 0.10 (0.33), residues: 270 loop : -1.24 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 394 HIS 0.002 0.000 HIS I 398 PHE 0.025 0.002 PHE B 188 TYR 0.022 0.002 TYR J 477 ARG 0.016 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 583 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6607 (m-30) cc_final: 0.6308 (m-30) REVERT: A 263 ASN cc_start: 0.8522 (t0) cc_final: 0.8242 (t0) REVERT: A 320 ASP cc_start: 0.7779 (t70) cc_final: 0.7501 (t0) REVERT: B 150 TYR cc_start: 0.7939 (m-80) cc_final: 0.7589 (m-80) REVERT: B 645 MET cc_start: 0.7342 (mmm) cc_final: 0.7122 (mmm) REVERT: D 24 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8059 (mtmm) REVERT: D 48 LEU cc_start: 0.8391 (tp) cc_final: 0.8030 (tp) REVERT: I 263 ASN cc_start: 0.8483 (t0) cc_final: 0.8120 (t0) REVERT: J 648 MET cc_start: 0.7893 (tpp) cc_final: 0.7620 (tpt) REVERT: E 108 VAL cc_start: 0.8201 (t) cc_final: 0.7916 (m) REVERT: E 139 ASP cc_start: 0.6554 (m-30) cc_final: 0.6334 (m-30) REVERT: E 263 ASN cc_start: 0.8701 (t0) cc_final: 0.8355 (t0) REVERT: E 320 ASP cc_start: 0.7578 (t70) cc_final: 0.7336 (t0) REVERT: E 469 THR cc_start: 0.7960 (p) cc_final: 0.7747 (p) REVERT: F 150 TYR cc_start: 0.8078 (m-80) cc_final: 0.7809 (m-80) outliers start: 2 outliers final: 0 residues processed: 585 average time/residue: 0.4125 time to fit residues: 398.8281 Evaluate side-chains 412 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 122 optimal weight: 0.4980 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33297 Z= 0.216 Angle : 0.540 9.128 45204 Z= 0.276 Chirality : 0.041 0.176 5334 Planarity : 0.004 0.050 5640 Dihedral : 7.039 71.252 4644 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.81 % Allowed : 9.29 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 4071 helix: 1.27 (0.10), residues: 2550 sheet: 0.17 (0.33), residues: 276 loop : -1.18 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 394 HIS 0.004 0.001 HIS L 45 PHE 0.016 0.002 PHE J 470 TYR 0.020 0.001 TYR J 477 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 464 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6765 (m-30) cc_final: 0.6458 (m-30) REVERT: A 263 ASN cc_start: 0.8757 (t0) cc_final: 0.8452 (t0) REVERT: A 268 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7715 (mm-40) REVERT: A 320 ASP cc_start: 0.7882 (t70) cc_final: 0.7579 (t0) REVERT: A 471 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7071 (mtt90) REVERT: B 150 TYR cc_start: 0.8253 (m-80) cc_final: 0.7679 (m-80) REVERT: B 426 ARG cc_start: 0.7398 (mtt90) cc_final: 0.7120 (mtt180) REVERT: C 56 ARG cc_start: 0.5639 (mtt-85) cc_final: 0.5423 (ptp90) REVERT: D 24 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8119 (mtmm) REVERT: D 48 LEU cc_start: 0.8748 (tp) cc_final: 0.8502 (tp) REVERT: D 65 MET cc_start: 0.7183 (ttt) cc_final: 0.6632 (ttp) REVERT: I 224 ASP cc_start: 0.8127 (t70) cc_final: 0.7726 (t0) REVERT: I 263 ASN cc_start: 0.8694 (t0) cc_final: 0.8269 (t0) REVERT: I 475 PHE cc_start: 0.8595 (t80) cc_final: 0.8132 (t80) REVERT: J 155 ILE cc_start: 0.8901 (mt) cc_final: 0.8674 (mm) REVERT: J 156 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: J 496 GLU cc_start: 0.6722 (tt0) cc_final: 0.6239 (tp30) REVERT: L 65 MET cc_start: 0.6687 (ttt) cc_final: 0.6358 (ttp) REVERT: E 108 VAL cc_start: 0.8123 (t) cc_final: 0.7838 (m) REVERT: E 224 ASP cc_start: 0.8239 (t70) cc_final: 0.8022 (t0) REVERT: E 263 ASN cc_start: 0.8975 (t0) cc_final: 0.8547 (t0) REVERT: E 320 ASP cc_start: 0.7665 (t70) cc_final: 0.7359 (t0) REVERT: E 354 ASN cc_start: 0.7681 (t0) cc_final: 0.7462 (t0) REVERT: F 150 TYR cc_start: 0.8315 (m-80) cc_final: 0.7843 (m-80) REVERT: F 156 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: F 598 ILE cc_start: 0.7395 (mm) cc_final: 0.7179 (mm) REVERT: F 703 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: H 65 MET cc_start: 0.6949 (ttt) cc_final: 0.6466 (ttp) outliers start: 64 outliers final: 49 residues processed: 503 average time/residue: 0.4291 time to fit residues: 357.6274 Evaluate side-chains 468 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 416 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 676 MET Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 306 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 368 optimal weight: 0.9980 chunk 398 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33297 Z= 0.228 Angle : 0.534 12.020 45204 Z= 0.270 Chirality : 0.041 0.157 5334 Planarity : 0.003 0.049 5640 Dihedral : 6.890 71.770 4644 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.15 % Allowed : 12.06 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.76 (0.13), residues: 4071 helix: 1.32 (0.10), residues: 2547 sheet: 0.15 (0.33), residues: 276 loop : -1.07 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.003 0.001 HIS E 531 PHE 0.020 0.001 PHE E 84 TYR 0.017 0.001 TYR J 477 ARG 0.008 0.000 ARG J 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 460 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6884 (m-30) cc_final: 0.6624 (m-30) REVERT: A 268 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7502 (mm-40) REVERT: A 320 ASP cc_start: 0.7922 (t70) cc_final: 0.7559 (t0) REVERT: A 471 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7151 (mtt90) REVERT: B 150 TYR cc_start: 0.8497 (m-80) cc_final: 0.7752 (m-80) REVERT: B 167 PHE cc_start: 0.7992 (m-10) cc_final: 0.7688 (m-10) REVERT: B 205 GLU cc_start: 0.7712 (tp30) cc_final: 0.7425 (tp30) REVERT: B 286 MET cc_start: 0.7822 (mmt) cc_final: 0.7442 (mmt) REVERT: B 308 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8171 (p) REVERT: B 703 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: D 24 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8238 (mtmm) REVERT: D 40 GLU cc_start: 0.7375 (pt0) cc_final: 0.7153 (mt-10) REVERT: D 47 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8278 (tm-30) REVERT: D 48 LEU cc_start: 0.8932 (tp) cc_final: 0.8617 (tp) REVERT: D 65 MET cc_start: 0.6950 (ttt) cc_final: 0.6483 (ttp) REVERT: I 224 ASP cc_start: 0.8213 (t70) cc_final: 0.7789 (t0) REVERT: I 263 ASN cc_start: 0.8885 (t0) cc_final: 0.8416 (t0) REVERT: I 475 PHE cc_start: 0.8625 (t80) cc_final: 0.8188 (t80) REVERT: J 389 MET cc_start: 0.8093 (tmm) cc_final: 0.7609 (tmm) REVERT: J 496 GLU cc_start: 0.6709 (tt0) cc_final: 0.6236 (tp30) REVERT: J 683 GLU cc_start: 0.7548 (mp0) cc_final: 0.7027 (mp0) REVERT: E 108 VAL cc_start: 0.8382 (t) cc_final: 0.8052 (m) REVERT: E 320 ASP cc_start: 0.7651 (t70) cc_final: 0.7298 (t0) REVERT: E 354 ASN cc_start: 0.7759 (t0) cc_final: 0.7529 (t0) REVERT: E 676 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8009 (mtp) REVERT: F 150 TYR cc_start: 0.8339 (m-80) cc_final: 0.7949 (m-80) REVERT: F 179 MET cc_start: 0.7549 (mtt) cc_final: 0.7294 (mtt) REVERT: F 188 PHE cc_start: 0.4821 (t80) cc_final: 0.4518 (t80) REVERT: F 598 ILE cc_start: 0.7425 (mm) cc_final: 0.7196 (mm) REVERT: F 703 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: H 65 MET cc_start: 0.6960 (ttt) cc_final: 0.6497 (ttp) outliers start: 76 outliers final: 57 residues processed: 502 average time/residue: 0.4164 time to fit residues: 350.5436 Evaluate side-chains 481 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 420 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 702 TYR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 247 optimal weight: 0.1980 chunk 369 optimal weight: 0.8980 chunk 391 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 350 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.206 Angle : 0.518 9.963 45204 Z= 0.262 Chirality : 0.040 0.194 5334 Planarity : 0.003 0.053 5640 Dihedral : 6.810 72.277 4644 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 13.74 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.86 (0.14), residues: 4071 helix: 1.41 (0.10), residues: 2544 sheet: 0.16 (0.33), residues: 276 loop : -1.05 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.003 0.001 HIS B 662 PHE 0.015 0.001 PHE E 323 TYR 0.013 0.001 TYR I 242 ARG 0.013 0.000 ARG I 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 454 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6976 (m-30) cc_final: 0.6658 (m-30) REVERT: A 268 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 320 ASP cc_start: 0.7834 (t70) cc_final: 0.7529 (t0) REVERT: A 471 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7138 (mtt180) REVERT: B 150 TYR cc_start: 0.8525 (m-80) cc_final: 0.7868 (m-80) REVERT: B 167 PHE cc_start: 0.8039 (m-10) cc_final: 0.7837 (m-10) REVERT: B 205 GLU cc_start: 0.7712 (tp30) cc_final: 0.7357 (tp30) REVERT: B 286 MET cc_start: 0.7820 (mmt) cc_final: 0.7423 (mmt) REVERT: B 308 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 703 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: D 24 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8286 (mtmm) REVERT: D 40 GLU cc_start: 0.7443 (pt0) cc_final: 0.7198 (mt-10) REVERT: D 48 LEU cc_start: 0.8912 (tp) cc_final: 0.8708 (tp) REVERT: D 65 MET cc_start: 0.6923 (ttt) cc_final: 0.6464 (ttp) REVERT: I 72 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8149 (mm) REVERT: I 140 PHE cc_start: 0.7530 (m-10) cc_final: 0.7293 (m-80) REVERT: I 263 ASN cc_start: 0.8967 (t0) cc_final: 0.8515 (t0) REVERT: I 475 PHE cc_start: 0.8578 (t80) cc_final: 0.8144 (t80) REVERT: I 570 MET cc_start: 0.7972 (ppp) cc_final: 0.7006 (ppp) REVERT: J 167 PHE cc_start: 0.8013 (m-10) cc_final: 0.7767 (m-10) REVERT: J 389 MET cc_start: 0.8088 (tmm) cc_final: 0.7565 (tmm) REVERT: J 496 GLU cc_start: 0.6708 (tt0) cc_final: 0.6238 (tp30) REVERT: E 108 VAL cc_start: 0.8177 (t) cc_final: 0.7846 (m) REVERT: E 320 ASP cc_start: 0.7653 (t70) cc_final: 0.7287 (t0) REVERT: E 354 ASN cc_start: 0.7710 (t0) cc_final: 0.7482 (t0) REVERT: E 633 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8145 (m) REVERT: F 150 TYR cc_start: 0.8309 (m-80) cc_final: 0.8093 (m-80) REVERT: F 156 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: F 188 PHE cc_start: 0.5359 (t80) cc_final: 0.5041 (t80) REVERT: F 286 MET cc_start: 0.7731 (mmt) cc_final: 0.7396 (mmt) REVERT: F 598 ILE cc_start: 0.7602 (mm) cc_final: 0.7392 (mm) REVERT: F 703 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8007 (mp10) outliers start: 92 outliers final: 66 residues processed: 512 average time/residue: 0.4184 time to fit residues: 358.7106 Evaluate side-chains 491 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 419 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 291 optimal weight: 0.5980 chunk 161 optimal weight: 7.9990 chunk 334 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 687 HIS J 268 GLN ** J 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33297 Z= 0.354 Angle : 0.616 8.995 45204 Z= 0.314 Chirality : 0.044 0.184 5334 Planarity : 0.004 0.048 5640 Dihedral : 7.027 81.146 4644 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.40 % Allowed : 15.15 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.38 (0.13), residues: 4071 helix: 1.06 (0.10), residues: 2541 sheet: -0.01 (0.32), residues: 267 loop : -1.28 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 431 HIS 0.004 0.001 HIS I 531 PHE 0.023 0.002 PHE F 413 TYR 0.016 0.001 TYR J 477 ARG 0.007 0.001 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 453 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6955 (m-30) cc_final: 0.6703 (m-30) REVERT: A 204 PHE cc_start: 0.7800 (m-80) cc_final: 0.7146 (t80) REVERT: A 320 ASP cc_start: 0.7916 (t70) cc_final: 0.7536 (t0) REVERT: A 472 ASN cc_start: 0.8106 (t0) cc_final: 0.7898 (t0) REVERT: B 150 TYR cc_start: 0.8539 (m-80) cc_final: 0.7981 (m-80) REVERT: B 205 GLU cc_start: 0.7817 (tp30) cc_final: 0.7487 (tp30) REVERT: B 286 MET cc_start: 0.7916 (mmt) cc_final: 0.7456 (mmt) REVERT: B 308 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 389 MET cc_start: 0.8115 (tmm) cc_final: 0.7769 (tmm) REVERT: B 592 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7868 (ttt-90) REVERT: B 703 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: D 24 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8250 (mtmm) REVERT: D 47 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8353 (tm-30) REVERT: I 72 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8267 (mm) REVERT: I 316 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6873 (tpp80) REVERT: I 320 ASP cc_start: 0.7985 (t70) cc_final: 0.7509 (t0) REVERT: I 389 MET cc_start: 0.7502 (tmm) cc_final: 0.7268 (tmm) REVERT: I 570 MET cc_start: 0.7763 (ppp) cc_final: 0.7302 (ppp) REVERT: I 587 PHE cc_start: 0.5806 (m-10) cc_final: 0.5605 (m-10) REVERT: J 167 PHE cc_start: 0.7919 (m-10) cc_final: 0.7653 (m-10) REVERT: J 286 MET cc_start: 0.7623 (mmt) cc_final: 0.7318 (mmt) REVERT: J 311 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7354 (tt) REVERT: J 389 MET cc_start: 0.8213 (tmm) cc_final: 0.7554 (tmm) REVERT: J 496 GLU cc_start: 0.6713 (tt0) cc_final: 0.6290 (tp30) REVERT: J 703 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: E 108 VAL cc_start: 0.8312 (t) cc_final: 0.7982 (m) REVERT: E 320 ASP cc_start: 0.7748 (t70) cc_final: 0.7353 (t0) REVERT: E 330 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: E 354 ASN cc_start: 0.7782 (t0) cc_final: 0.7529 (t0) REVERT: E 471 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: F 188 PHE cc_start: 0.5217 (t80) cc_final: 0.4981 (t80) REVERT: F 286 MET cc_start: 0.8030 (mmt) cc_final: 0.7776 (mmt) REVERT: F 535 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7981 (pt) REVERT: F 703 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: G 34 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6822 (mtm-85) REVERT: H 47 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8085 (tm-30) outliers start: 120 outliers final: 86 residues processed: 536 average time/residue: 0.4640 time to fit residues: 418.5136 Evaluate side-chains 502 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 408 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 667 VAL Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 4.9990 chunk 352 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33297 Z= 0.200 Angle : 0.528 9.720 45204 Z= 0.269 Chirality : 0.041 0.147 5334 Planarity : 0.003 0.051 5640 Dihedral : 6.810 77.166 4644 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.63 % Allowed : 17.22 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 4071 helix: 1.35 (0.10), residues: 2544 sheet: -0.08 (0.32), residues: 273 loop : -1.17 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 307 HIS 0.005 0.001 HIS E 185 PHE 0.031 0.001 PHE A 475 TYR 0.013 0.001 TYR J 288 ARG 0.004 0.000 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 454 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6920 (m-30) cc_final: 0.6707 (m-30) REVERT: A 170 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6683 (tp) REVERT: A 320 ASP cc_start: 0.7949 (t70) cc_final: 0.7561 (t0) REVERT: A 472 ASN cc_start: 0.7996 (t0) cc_final: 0.7727 (t0) REVERT: A 570 MET cc_start: 0.8129 (ppp) cc_final: 0.7365 (ppp) REVERT: B 150 TYR cc_start: 0.8433 (m-80) cc_final: 0.7913 (m-80) REVERT: B 205 GLU cc_start: 0.7690 (tp30) cc_final: 0.7329 (tp30) REVERT: B 286 MET cc_start: 0.7798 (mmt) cc_final: 0.7485 (mmt) REVERT: B 308 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 703 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: D 24 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8267 (mtmm) REVERT: I 29 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7021 (tm-30) REVERT: I 72 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8162 (mm) REVERT: I 77 TRP cc_start: 0.8555 (t-100) cc_final: 0.8007 (t-100) REVERT: I 170 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6472 (tp) REVERT: I 316 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6858 (tpp80) REVERT: I 320 ASP cc_start: 0.7944 (t70) cc_final: 0.7459 (t0) REVERT: I 389 MET cc_start: 0.7454 (tmm) cc_final: 0.7231 (tmm) REVERT: I 472 ASN cc_start: 0.7853 (m-40) cc_final: 0.7092 (t0) REVERT: I 570 MET cc_start: 0.7855 (ppp) cc_final: 0.7404 (ppp) REVERT: J 167 PHE cc_start: 0.7893 (m-10) cc_final: 0.7664 (m-10) REVERT: J 211 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mt) REVERT: J 286 MET cc_start: 0.7608 (mmt) cc_final: 0.7321 (mmt) REVERT: J 308 SER cc_start: 0.8914 (t) cc_final: 0.8313 (p) REVERT: J 389 MET cc_start: 0.8032 (tmm) cc_final: 0.7466 (tmm) REVERT: J 496 GLU cc_start: 0.6770 (tt0) cc_final: 0.6297 (tp30) REVERT: E 108 VAL cc_start: 0.8222 (t) cc_final: 0.7918 (m) REVERT: E 170 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6531 (tp) REVERT: E 320 ASP cc_start: 0.7671 (t70) cc_final: 0.7293 (t0) REVERT: E 330 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: E 354 ASN cc_start: 0.7750 (t0) cc_final: 0.7496 (t0) REVERT: E 471 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6985 (mtt90) REVERT: F 156 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: F 188 PHE cc_start: 0.5345 (t80) cc_final: 0.4998 (t80) REVERT: F 286 MET cc_start: 0.7856 (mmt) cc_final: 0.7589 (mmt) REVERT: F 477 TYR cc_start: 0.8185 (m-80) cc_final: 0.7946 (m-10) REVERT: F 703 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: G 34 ARG cc_start: 0.7215 (mtm110) cc_final: 0.6885 (mtm-85) outliers start: 93 outliers final: 63 residues processed: 513 average time/residue: 0.4074 time to fit residues: 347.3597 Evaluate side-chains 494 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 421 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 286 optimal weight: 0.0470 chunk 221 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 390 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.211 Angle : 0.539 9.330 45204 Z= 0.273 Chirality : 0.041 0.213 5334 Planarity : 0.003 0.051 5640 Dihedral : 6.775 78.885 4644 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.86 % Allowed : 17.53 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.77 (0.13), residues: 4071 helix: 1.42 (0.10), residues: 2541 sheet: -0.09 (0.32), residues: 273 loop : -1.20 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.003 0.001 HIS F 662 PHE 0.016 0.001 PHE E 323 TYR 0.014 0.001 TYR E 12 ARG 0.010 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 440 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6670 (tp) REVERT: A 320 ASP cc_start: 0.7949 (t70) cc_final: 0.7558 (t0) REVERT: A 570 MET cc_start: 0.8097 (ppp) cc_final: 0.7747 (ppp) REVERT: B 150 TYR cc_start: 0.8468 (m-80) cc_final: 0.7941 (m-80) REVERT: B 308 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 389 MET cc_start: 0.8047 (tmm) cc_final: 0.7817 (tmm) REVERT: B 703 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: D 24 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8261 (mtmm) REVERT: I 72 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8152 (mm) REVERT: I 77 TRP cc_start: 0.8592 (t-100) cc_final: 0.8068 (t-100) REVERT: I 170 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6449 (tp) REVERT: I 320 ASP cc_start: 0.7936 (t70) cc_final: 0.7469 (t0) REVERT: I 389 MET cc_start: 0.7463 (tmm) cc_final: 0.7232 (tmm) REVERT: I 471 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7164 (mtm-85) REVERT: I 472 ASN cc_start: 0.7908 (m-40) cc_final: 0.7116 (t0) REVERT: I 570 MET cc_start: 0.7875 (ppp) cc_final: 0.7502 (ppp) REVERT: J 167 PHE cc_start: 0.7994 (m-10) cc_final: 0.7738 (m-10) REVERT: J 286 MET cc_start: 0.7630 (mmt) cc_final: 0.7352 (mmt) REVERT: J 308 SER cc_start: 0.8929 (t) cc_final: 0.8448 (p) REVERT: J 389 MET cc_start: 0.8032 (tmm) cc_final: 0.7477 (tmm) REVERT: J 496 GLU cc_start: 0.6794 (tt0) cc_final: 0.6226 (tp30) REVERT: E 48 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7767 (mm) REVERT: E 108 VAL cc_start: 0.8309 (t) cc_final: 0.8039 (m) REVERT: E 170 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6535 (tp) REVERT: E 320 ASP cc_start: 0.7668 (t70) cc_final: 0.7290 (t0) REVERT: E 330 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: E 354 ASN cc_start: 0.7793 (t0) cc_final: 0.7489 (t0) REVERT: E 471 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6804 (mtt90) REVERT: F 156 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: F 188 PHE cc_start: 0.5348 (t80) cc_final: 0.5078 (t80) REVERT: F 205 GLU cc_start: 0.8089 (tp30) cc_final: 0.7685 (tp30) REVERT: F 286 MET cc_start: 0.7852 (mmt) cc_final: 0.7614 (mmt) REVERT: F 415 MET cc_start: 0.8100 (mmt) cc_final: 0.7620 (mtp) REVERT: F 703 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7943 (mp10) outliers start: 101 outliers final: 76 residues processed: 506 average time/residue: 0.4112 time to fit residues: 347.0680 Evaluate side-chains 501 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 415 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 0.0370 chunk 155 optimal weight: 0.5980 chunk 233 optimal weight: 0.7980 chunk 117 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 248 optimal weight: 0.0020 chunk 265 optimal weight: 0.3980 chunk 192 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 306 optimal weight: 0.6980 overall best weight: 0.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33297 Z= 0.141 Angle : 0.518 10.589 45204 Z= 0.260 Chirality : 0.040 0.207 5334 Planarity : 0.003 0.049 5640 Dihedral : 6.558 72.673 4644 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.24 % Allowed : 18.52 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 4071 helix: 1.63 (0.11), residues: 2562 sheet: 0.20 (0.32), residues: 276 loop : -1.10 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 307 HIS 0.002 0.000 HIS F 662 PHE 0.014 0.001 PHE I 69 TYR 0.023 0.001 TYR F 477 ARG 0.008 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 481 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.7662 (m-80) cc_final: 0.7095 (t80) REVERT: A 320 ASP cc_start: 0.7870 (t70) cc_final: 0.7487 (t0) REVERT: A 384 ILE cc_start: 0.8238 (mm) cc_final: 0.8013 (mt) REVERT: A 570 MET cc_start: 0.8165 (ppp) cc_final: 0.7886 (ppp) REVERT: B 150 TYR cc_start: 0.8339 (m-80) cc_final: 0.7878 (m-80) REVERT: B 205 GLU cc_start: 0.7735 (tp30) cc_final: 0.7424 (tp30) REVERT: B 211 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7426 (mm) REVERT: B 286 MET cc_start: 0.7890 (mmt) cc_final: 0.7589 (mmt) REVERT: B 389 MET cc_start: 0.8092 (tmm) cc_final: 0.7829 (tmm) REVERT: B 643 ILE cc_start: 0.8235 (mm) cc_final: 0.7792 (mm) REVERT: B 703 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: D 24 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8184 (mtmm) REVERT: D 47 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 50 GLU cc_start: 0.7578 (tp30) cc_final: 0.7373 (tp30) REVERT: I 29 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7062 (tm-30) REVERT: I 72 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8006 (mm) REVERT: I 77 TRP cc_start: 0.8505 (t-100) cc_final: 0.8053 (t-100) REVERT: I 86 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6967 (tt) REVERT: I 88 LYS cc_start: 0.8085 (tptm) cc_final: 0.7810 (ttpp) REVERT: I 384 ILE cc_start: 0.8183 (mm) cc_final: 0.7967 (mt) REVERT: I 472 ASN cc_start: 0.7502 (m-40) cc_final: 0.7089 (t0) REVERT: I 570 MET cc_start: 0.7836 (ppp) cc_final: 0.7491 (ppp) REVERT: J 188 PHE cc_start: 0.5296 (t80) cc_final: 0.5080 (t80) REVERT: J 308 SER cc_start: 0.8970 (t) cc_final: 0.8418 (p) REVERT: J 389 MET cc_start: 0.7993 (tmm) cc_final: 0.7524 (tmm) REVERT: J 496 GLU cc_start: 0.6677 (tt0) cc_final: 0.6174 (tp30) REVERT: L 65 MET cc_start: 0.6494 (ttt) cc_final: 0.5979 (ttp) REVERT: E 48 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7654 (mm) REVERT: E 108 VAL cc_start: 0.8240 (t) cc_final: 0.7995 (m) REVERT: E 320 ASP cc_start: 0.7457 (t70) cc_final: 0.7211 (t0) REVERT: E 676 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: F 156 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: F 188 PHE cc_start: 0.5507 (t80) cc_final: 0.5213 (t80) REVERT: F 205 GLU cc_start: 0.8019 (tp30) cc_final: 0.7558 (tp30) REVERT: F 286 MET cc_start: 0.7860 (mmt) cc_final: 0.7636 (mmt) REVERT: F 415 MET cc_start: 0.7880 (mmt) cc_final: 0.7378 (mtp) REVERT: F 703 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7954 (mp10) outliers start: 79 outliers final: 54 residues processed: 530 average time/residue: 0.4140 time to fit residues: 366.0174 Evaluate side-chains 501 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 439 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 570 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 0.9980 chunk 373 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 363 optimal weight: 0.9990 chunk 218 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 328 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 362 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.182 Angle : 0.536 9.952 45204 Z= 0.267 Chirality : 0.040 0.215 5334 Planarity : 0.003 0.051 5640 Dihedral : 6.576 77.060 4644 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.93 % Allowed : 19.48 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 4071 helix: 1.65 (0.11), residues: 2544 sheet: 0.21 (0.32), residues: 276 loop : -1.14 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.002 0.000 HIS F 662 PHE 0.023 0.001 PHE B 413 TYR 0.014 0.001 TYR J 288 ARG 0.007 0.000 ARG E 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 452 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7989 (tptm) cc_final: 0.7653 (ttpp) REVERT: A 268 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7432 (mm-40) REVERT: A 320 ASP cc_start: 0.7913 (t70) cc_final: 0.7519 (t0) REVERT: A 384 ILE cc_start: 0.8292 (mm) cc_final: 0.8076 (mt) REVERT: B 150 TYR cc_start: 0.8349 (m-80) cc_final: 0.7847 (m-80) REVERT: B 205 GLU cc_start: 0.7848 (tp30) cc_final: 0.7476 (tp30) REVERT: B 211 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7400 (mm) REVERT: B 286 MET cc_start: 0.7967 (mmt) cc_final: 0.7678 (mmt) REVERT: B 308 SER cc_start: 0.8971 (t) cc_final: 0.8436 (p) REVERT: B 389 MET cc_start: 0.8094 (tmm) cc_final: 0.7837 (tmm) REVERT: B 643 ILE cc_start: 0.8267 (mm) cc_final: 0.7828 (mm) REVERT: D 47 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8162 (tm-30) REVERT: D 50 GLU cc_start: 0.7634 (tp30) cc_final: 0.7426 (tp30) REVERT: I 77 TRP cc_start: 0.8545 (t-100) cc_final: 0.8069 (t-100) REVERT: I 88 LYS cc_start: 0.8100 (tptm) cc_final: 0.7800 (ttpp) REVERT: I 384 ILE cc_start: 0.8189 (mm) cc_final: 0.7948 (mt) REVERT: I 472 ASN cc_start: 0.7864 (m-40) cc_final: 0.7077 (t0) REVERT: I 570 MET cc_start: 0.7788 (ppp) cc_final: 0.7433 (ppp) REVERT: J 268 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6857 (mm-40) REVERT: J 308 SER cc_start: 0.8990 (t) cc_final: 0.8424 (p) REVERT: J 389 MET cc_start: 0.8056 (tmm) cc_final: 0.7545 (tmm) REVERT: J 496 GLU cc_start: 0.6707 (tt0) cc_final: 0.6196 (tp30) REVERT: L 65 MET cc_start: 0.6633 (ttt) cc_final: 0.6098 (ttp) REVERT: E 48 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7733 (mm) REVERT: E 108 VAL cc_start: 0.8239 (t) cc_final: 0.7955 (m) REVERT: E 320 ASP cc_start: 0.7620 (t70) cc_final: 0.7256 (t0) REVERT: F 156 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: F 188 PHE cc_start: 0.5404 (t80) cc_final: 0.5167 (t80) REVERT: F 205 GLU cc_start: 0.8042 (tp30) cc_final: 0.7620 (tp30) REVERT: F 415 MET cc_start: 0.8081 (mmt) cc_final: 0.7592 (mtp) REVERT: F 703 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7951 (mp10) outliers start: 68 outliers final: 58 residues processed: 490 average time/residue: 0.4197 time to fit residues: 343.6376 Evaluate side-chains 497 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 435 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 570 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 0.9990 chunk 384 optimal weight: 0.9990 chunk 234 optimal weight: 0.6980 chunk 182 optimal weight: 7.9990 chunk 267 optimal weight: 0.8980 chunk 403 optimal weight: 0.9980 chunk 371 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 248 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.184 Angle : 0.547 12.283 45204 Z= 0.272 Chirality : 0.040 0.223 5334 Planarity : 0.003 0.053 5640 Dihedral : 6.570 77.378 4644 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.04 % Allowed : 19.63 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 4071 helix: 1.65 (0.11), residues: 2544 sheet: 0.21 (0.32), residues: 276 loop : -1.14 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.002 0.000 HIS F 662 PHE 0.029 0.001 PHE F 413 TYR 0.017 0.001 TYR J 288 ARG 0.007 0.000 ARG H 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 451 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8135 (tptm) cc_final: 0.7685 (ttpp) REVERT: A 268 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 320 ASP cc_start: 0.7909 (t70) cc_final: 0.7490 (t0) REVERT: A 384 ILE cc_start: 0.8288 (mm) cc_final: 0.8083 (mt) REVERT: A 471 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7482 (mtm-85) REVERT: B 150 TYR cc_start: 0.8353 (m-80) cc_final: 0.7862 (m-80) REVERT: B 205 GLU cc_start: 0.7893 (tp30) cc_final: 0.7479 (tp30) REVERT: B 211 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7405 (mm) REVERT: B 286 MET cc_start: 0.7949 (mmt) cc_final: 0.7626 (mmp) REVERT: B 308 SER cc_start: 0.8979 (t) cc_final: 0.8447 (p) REVERT: B 389 MET cc_start: 0.8093 (tmm) cc_final: 0.7823 (tmm) REVERT: B 643 ILE cc_start: 0.8273 (mm) cc_final: 0.7838 (mm) REVERT: D 47 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 50 GLU cc_start: 0.7671 (tp30) cc_final: 0.7466 (tp30) REVERT: I 77 TRP cc_start: 0.8537 (t-100) cc_final: 0.8052 (t-100) REVERT: I 88 LYS cc_start: 0.8114 (tptm) cc_final: 0.7808 (ttpp) REVERT: I 320 ASP cc_start: 0.7895 (t70) cc_final: 0.7411 (t0) REVERT: I 384 ILE cc_start: 0.8167 (mm) cc_final: 0.7938 (mt) REVERT: I 472 ASN cc_start: 0.7834 (m-40) cc_final: 0.7042 (t0) REVERT: I 570 MET cc_start: 0.7888 (ppp) cc_final: 0.7549 (ppp) REVERT: J 308 SER cc_start: 0.9008 (t) cc_final: 0.8459 (p) REVERT: J 389 MET cc_start: 0.8038 (tmm) cc_final: 0.7495 (tmm) REVERT: J 496 GLU cc_start: 0.6721 (tt0) cc_final: 0.6207 (tp30) REVERT: L 65 MET cc_start: 0.6624 (ttt) cc_final: 0.6112 (ttp) REVERT: E 48 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7736 (mm) REVERT: E 108 VAL cc_start: 0.8251 (t) cc_final: 0.7961 (m) REVERT: E 320 ASP cc_start: 0.7641 (t70) cc_final: 0.7270 (t0) REVERT: F 156 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: F 188 PHE cc_start: 0.5499 (t80) cc_final: 0.5152 (t80) REVERT: F 205 GLU cc_start: 0.8032 (tp30) cc_final: 0.7602 (tp30) REVERT: F 415 MET cc_start: 0.7990 (mmt) cc_final: 0.7516 (mtp) REVERT: F 703 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7991 (mp10) outliers start: 72 outliers final: 64 residues processed: 490 average time/residue: 0.4170 time to fit residues: 343.0569 Evaluate side-chains 510 residues out of total 3582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 442 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 286 MET Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 570 MET Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 570 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 0.8980 chunk 342 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 0.0010 chunk 321 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 268 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120213 restraints weight = 46411.857| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.47 r_work: 0.3358 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.179 Angle : 0.547 10.487 45204 Z= 0.273 Chirality : 0.040 0.217 5334 Planarity : 0.003 0.053 5640 Dihedral : 6.540 77.231 4644 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.21 % Allowed : 19.65 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 4071 helix: 1.68 (0.11), residues: 2544 sheet: 0.23 (0.32), residues: 276 loop : -1.13 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.003 0.000 HIS F 662 PHE 0.027 0.001 PHE I 69 TYR 0.017 0.001 TYR J 288 ARG 0.007 0.000 ARG H 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6930.59 seconds wall clock time: 127 minutes 25.59 seconds (7645.59 seconds total)