Starting phenix.real_space_refine on Fri Mar 15 10:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/03_2024/7lgw_23331_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 2 4.86 5 C 7766 2.51 5 N 1690 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B GLU 721": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11390 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 459 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 17, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 19} Classifications: {'undetermined': 48} Link IDs: {None: 47} Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 449 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 16, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 19} Classifications: {'undetermined': 47} Link IDs: {None: 46} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 6.73, per 1000 atoms: 0.59 Number of scatterers: 11390 At special positions: 0 Unit cell: (102.16, 117.777, 113.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 48 16.00 O 1884 8.00 N 1690 7.00 C 7766 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: 4.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 6 sheets defined 64.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.752A pdb=" N ARG A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.904A pdb=" N TRP A 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 104 removed outlier: 5.545A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.505A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 169 through 195 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 242 through 256 removed outlier: 5.100A pdb=" N LYS A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 281 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 333 through 365 removed outlier: 4.698A pdb=" N HIS A 337 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR A 340 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL A 341 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 349 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 353 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 356 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 358 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.792A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 437 through 464 removed outlier: 4.047A pdb=" N LYS A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 486 through 504 removed outlier: 4.029A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 546 through 559 removed outlier: 4.823A pdb=" N ASP A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 627 through 632 removed outlier: 4.191A pdb=" N PHE A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 669 Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.772A pdb=" N GLU A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 706 through 724 Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.752A pdb=" N ARG B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.904A pdb=" N TRP B 70 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 104 removed outlier: 5.544A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.505A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 169 through 195 Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 207 through 224 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 242 through 256 removed outlier: 5.100A pdb=" N LYS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASN B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 281 Processing helix chain 'B' and resid 292 through 307 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 333 through 365 removed outlier: 4.698A pdb=" N HIS B 337 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR B 340 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL B 341 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 346 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 349 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 350 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 353 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 356 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 357 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 358 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.793A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 437 through 464 removed outlier: 4.047A pdb=" N LYS B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY B 450 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Proline residue: B 459 - end of helix Processing helix chain 'B' and resid 466 through 481 Processing helix chain 'B' and resid 486 through 504 removed outlier: 4.029A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 No H-bonds generated for 'chain 'B' and resid 523 through 526' Processing helix chain 'B' and resid 546 through 559 removed outlier: 4.823A pdb=" N ASP B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 578 Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.193A pdb=" N PHE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 691 through 694 removed outlier: 3.772A pdb=" N GLU B 694 " --> pdb=" O ARG B 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 694' Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 706 through 724 Processing sheet with id= A, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.633A pdb=" N SER A 133 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.715A pdb=" N THR A 641 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 538 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 643 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE A 540 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP A 645 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 673 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 644 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A 675 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 511 through 513 Processing sheet with id= D, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.633A pdb=" N SER B 133 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.715A pdb=" N THR B 641 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE B 538 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 643 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE B 540 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP B 645 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B 673 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU B 644 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR B 675 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 511 through 513 558 hydrogen bonds defined for protein. 1506 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: 3.24 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3238 1.34 - 1.46: 2221 1.46 - 1.58: 5972 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11509 Sorted by residual: bond pdb=" CB GLU B 721 " pdb=" CG GLU B 721 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" CB GLU A 721 " pdb=" CG GLU A 721 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" C3 CLR A 802 " pdb=" O1 CLR A 802 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C3 CLR B 802 " pdb=" O1 CLR B 802 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" CG GLU B 721 " pdb=" CD GLU B 721 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.20e-01 ... (remaining 11504 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.28: 315 106.28 - 113.23: 6669 113.23 - 120.18: 3847 120.18 - 127.13: 4368 127.13 - 134.08: 97 Bond angle restraints: 15296 Sorted by residual: angle pdb=" N GLU B 527 " pdb=" CA GLU B 527 " pdb=" CB GLU B 527 " ideal model delta sigma weight residual 114.27 108.71 5.56 1.64e+00 3.72e-01 1.15e+01 angle pdb=" N GLU A 527 " pdb=" CA GLU A 527 " pdb=" CB GLU A 527 " ideal model delta sigma weight residual 114.27 108.72 5.55 1.64e+00 3.72e-01 1.14e+01 angle pdb=" N ASN A 548 " pdb=" CA ASN A 548 " pdb=" C ASN A 548 " ideal model delta sigma weight residual 114.75 110.90 3.85 1.26e+00 6.30e-01 9.33e+00 angle pdb=" N ASN B 548 " pdb=" CA ASN B 548 " pdb=" C ASN B 548 " ideal model delta sigma weight residual 114.75 110.92 3.83 1.26e+00 6.30e-01 9.25e+00 angle pdb=" CB MET A 575 " pdb=" CG MET A 575 " pdb=" SD MET A 575 " ideal model delta sigma weight residual 112.70 120.73 -8.03 3.00e+00 1.11e-01 7.16e+00 ... (remaining 15291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 6485 16.35 - 32.70: 439 32.70 - 49.05: 87 49.05 - 65.40: 30 65.40 - 81.75: 4 Dihedral angle restraints: 7045 sinusoidal: 3121 harmonic: 3924 Sorted by residual: dihedral pdb=" CA GLU A 527 " pdb=" C GLU A 527 " pdb=" N GLU A 528 " pdb=" CA GLU A 528 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU B 527 " pdb=" C GLU B 527 " pdb=" N GLU B 528 " pdb=" CA GLU B 528 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 7042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 936 0.028 - 0.056: 507 0.056 - 0.084: 188 0.084 - 0.112: 90 0.112 - 0.140: 23 Chirality restraints: 1744 Sorted by residual: chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1741 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 686 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CG ASP A 686 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 686 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 686 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 686 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" CG ASP B 686 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP B 686 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 686 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 53 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO B 54 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.019 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 487 2.73 - 3.27: 11317 3.27 - 3.81: 18515 3.81 - 4.36: 23969 4.36 - 4.90: 39874 Nonbonded interactions: 94162 Sorted by model distance: nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.184 2.440 nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.184 2.440 nonbonded pdb=" OD1 ASP A 645 " pdb=" OG1 THR A 647 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 645 " pdb=" OG1 THR B 647 " model vdw 2.232 2.440 nonbonded pdb=" O VAL B 402 " pdb=" OG1 THR B 406 " model vdw 2.257 2.440 ... (remaining 94157 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' and (resid 13 through 725 or resid 801 through 835 or resid 841 throu \ gh 847)) selection = (chain 'B' and (resid 13 through 725 or resid 801 through 835 or resid 841 throu \ gh 847)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.330 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 32.440 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11509 Z= 0.223 Angle : 0.955 8.029 15296 Z= 0.403 Chirality : 0.042 0.140 1744 Planarity : 0.004 0.034 1808 Dihedral : 12.091 81.749 4533 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.71 % Allowed : 0.71 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1352 helix: 1.36 (0.17), residues: 904 sheet: 1.54 (0.72), residues: 50 loop : -0.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.004 0.001 HIS B 707 PHE 0.014 0.001 PHE A 625 TYR 0.020 0.001 TYR A 79 ARG 0.006 0.001 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.172 Fit side-chains REVERT: A 316 ASP cc_start: 0.8311 (m-30) cc_final: 0.8035 (m-30) REVERT: A 463 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7484 (mtp180) REVERT: B 316 ASP cc_start: 0.8308 (m-30) cc_final: 0.8030 (m-30) REVERT: B 463 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7458 (mtp180) outliers start: 8 outliers final: 0 residues processed: 137 average time/residue: 1.2405 time to fit residues: 184.2364 Evaluate side-chains 100 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 0.0370 overall best weight: 2.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 454 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11509 Z= 0.252 Angle : 0.511 6.209 15296 Z= 0.257 Chirality : 0.042 0.130 1744 Planarity : 0.004 0.040 1808 Dihedral : 7.254 55.101 2163 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.41 % Allowed : 6.70 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.23), residues: 1352 helix: 1.28 (0.17), residues: 904 sheet: 1.68 (0.72), residues: 50 loop : -0.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.003 0.001 HIS B 640 PHE 0.014 0.001 PHE A 111 TYR 0.015 0.002 TYR A 16 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.181 Fit side-chains REVERT: A 267 MET cc_start: 0.7404 (ttp) cc_final: 0.7187 (ttt) REVERT: A 271 LEU cc_start: 0.8227 (mt) cc_final: 0.8009 (mp) REVERT: A 316 ASP cc_start: 0.8378 (m-30) cc_final: 0.8035 (m-30) REVERT: A 463 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7423 (mtp180) REVERT: A 572 ARG cc_start: 0.7336 (mtm110) cc_final: 0.7126 (mtm110) REVERT: A 682 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: B 267 MET cc_start: 0.7449 (ttp) cc_final: 0.7211 (ttt) REVERT: B 271 LEU cc_start: 0.8317 (mt) cc_final: 0.8107 (mp) REVERT: B 316 ASP cc_start: 0.8360 (m-30) cc_final: 0.8013 (m-30) REVERT: B 463 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7499 (mtp180) REVERT: B 682 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7112 (tt0) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 1.2844 time to fit residues: 153.5072 Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11509 Z= 0.118 Angle : 0.427 7.601 15296 Z= 0.215 Chirality : 0.039 0.128 1744 Planarity : 0.003 0.035 1808 Dihedral : 6.395 58.096 2163 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 8.29 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1352 helix: 1.61 (0.18), residues: 894 sheet: 1.88 (0.72), residues: 50 loop : -0.23 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.002 0.001 HIS A 220 PHE 0.022 0.001 PHE A 241 TYR 0.011 0.001 TYR A 16 ARG 0.002 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.225 Fit side-chains REVERT: A 267 MET cc_start: 0.7352 (ttp) cc_final: 0.7150 (ttt) REVERT: A 316 ASP cc_start: 0.8330 (m-30) cc_final: 0.7987 (m-30) REVERT: A 463 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7482 (mtp180) REVERT: B 267 MET cc_start: 0.7358 (ttp) cc_final: 0.7122 (ttp) REVERT: B 316 ASP cc_start: 0.8335 (m-30) cc_final: 0.7987 (m-30) REVERT: B 463 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7482 (mtp180) REVERT: B 682 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7087 (tt0) outliers start: 13 outliers final: 5 residues processed: 112 average time/residue: 1.1180 time to fit residues: 137.3328 Evaluate side-chains 98 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11509 Z= 0.331 Angle : 0.555 7.797 15296 Z= 0.278 Chirality : 0.043 0.129 1744 Planarity : 0.005 0.041 1808 Dihedral : 7.918 58.363 2163 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.12 % Allowed : 8.99 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1352 helix: 1.17 (0.17), residues: 898 sheet: 3.13 (0.73), residues: 38 loop : -0.41 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 472 HIS 0.005 0.001 HIS B 25 PHE 0.018 0.002 PHE A 241 TYR 0.017 0.002 TYR B 16 ARG 0.003 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.227 Fit side-chains REVERT: A 257 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8184 (pt) REVERT: A 267 MET cc_start: 0.7301 (ttp) cc_final: 0.7078 (ttp) REVERT: A 316 ASP cc_start: 0.8388 (m-30) cc_final: 0.8045 (m-30) REVERT: A 463 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7497 (mtp180) REVERT: A 682 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: B 262 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 310 LYS cc_start: 0.7147 (tttt) cc_final: 0.6943 (tptt) REVERT: B 316 ASP cc_start: 0.8411 (m-30) cc_final: 0.8078 (m-30) REVERT: B 463 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7463 (mtp180) REVERT: B 682 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7067 (tt0) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 1.2481 time to fit residues: 153.7181 Evaluate side-chains 112 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11509 Z= 0.217 Angle : 0.494 10.114 15296 Z= 0.246 Chirality : 0.041 0.129 1744 Planarity : 0.004 0.036 1808 Dihedral : 7.530 59.094 2163 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.20 % Allowed : 9.79 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1352 helix: 1.20 (0.17), residues: 898 sheet: 3.12 (0.72), residues: 38 loop : -0.33 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.003 0.001 HIS A 640 PHE 0.014 0.001 PHE A 241 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.170 Fit side-chains REVERT: A 257 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8206 (pt) REVERT: A 310 LYS cc_start: 0.7120 (tttt) cc_final: 0.6912 (tptt) REVERT: A 316 ASP cc_start: 0.8391 (m-30) cc_final: 0.8038 (m-30) REVERT: A 463 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7470 (mtp180) REVERT: A 682 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: B 262 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7674 (tp) REVERT: B 316 ASP cc_start: 0.8377 (m-30) cc_final: 0.8123 (m-30) REVERT: B 463 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7520 (mtp180) REVERT: B 682 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7044 (tt0) outliers start: 25 outliers final: 14 residues processed: 113 average time/residue: 1.2174 time to fit residues: 149.5037 Evaluate side-chains 116 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11509 Z= 0.294 Angle : 0.528 7.792 15296 Z= 0.264 Chirality : 0.043 0.128 1744 Planarity : 0.004 0.038 1808 Dihedral : 7.980 59.354 2163 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.12 % Allowed : 10.49 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1352 helix: 1.07 (0.17), residues: 898 sheet: 3.04 (0.72), residues: 38 loop : -0.41 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 472 HIS 0.004 0.001 HIS B 640 PHE 0.015 0.002 PHE A 111 TYR 0.016 0.001 TYR B 16 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.307 Fit side-chains REVERT: A 316 ASP cc_start: 0.8390 (m-30) cc_final: 0.8118 (m-30) REVERT: A 463 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7468 (mtp180) REVERT: A 682 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: B 262 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7720 (tp) REVERT: B 316 ASP cc_start: 0.8379 (m-30) cc_final: 0.8121 (m-30) REVERT: B 463 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7482 (mtp180) REVERT: B 682 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7130 (tt0) outliers start: 24 outliers final: 17 residues processed: 111 average time/residue: 1.3045 time to fit residues: 157.3159 Evaluate side-chains 118 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11509 Z= 0.127 Angle : 0.464 11.161 15296 Z= 0.228 Chirality : 0.040 0.126 1744 Planarity : 0.003 0.036 1808 Dihedral : 7.050 58.393 2163 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.85 % Allowed : 10.93 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1352 helix: 1.32 (0.17), residues: 904 sheet: 3.20 (0.72), residues: 38 loop : -0.35 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 PHE 0.016 0.001 PHE A 269 TYR 0.012 0.001 TYR B 16 ARG 0.002 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.118 Fit side-chains REVERT: A 316 ASP cc_start: 0.8393 (m-30) cc_final: 0.8140 (m-30) REVERT: A 463 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7485 (mtp180) REVERT: A 682 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: B 262 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7644 (tp) REVERT: B 316 ASP cc_start: 0.8376 (m-30) cc_final: 0.8133 (m-30) REVERT: B 463 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7477 (mtp180) REVERT: B 682 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7085 (tt0) outliers start: 21 outliers final: 11 residues processed: 107 average time/residue: 1.0840 time to fit residues: 127.4632 Evaluate side-chains 107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.0030 chunk 114 optimal weight: 2.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11509 Z= 0.378 Angle : 0.584 13.792 15296 Z= 0.286 Chirality : 0.045 0.149 1744 Planarity : 0.005 0.046 1808 Dihedral : 8.067 59.720 2163 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.29 % Allowed : 11.02 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1352 helix: 0.99 (0.17), residues: 904 sheet: 3.07 (0.74), residues: 38 loop : -0.49 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 472 HIS 0.004 0.001 HIS B 640 PHE 0.017 0.002 PHE B 111 TYR 0.016 0.002 TYR B 16 ARG 0.003 0.001 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.227 Fit side-chains REVERT: A 316 ASP cc_start: 0.8372 (m-30) cc_final: 0.8107 (m-30) REVERT: A 463 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7467 (mtp180) REVERT: A 682 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: B 262 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7786 (tt) REVERT: B 316 ASP cc_start: 0.8427 (m-30) cc_final: 0.8181 (m-30) REVERT: B 463 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7466 (mtp180) REVERT: B 682 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7125 (tt0) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 1.2213 time to fit residues: 146.8666 Evaluate side-chains 116 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11509 Z= 0.172 Angle : 0.491 13.104 15296 Z= 0.240 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.038 1808 Dihedral : 7.441 59.995 2163 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.68 % Allowed : 11.64 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1352 helix: 1.16 (0.17), residues: 904 sheet: 3.14 (0.73), residues: 38 loop : -0.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.002 0.001 HIS B 220 PHE 0.012 0.001 PHE A 241 TYR 0.013 0.001 TYR B 16 ARG 0.001 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.236 Fit side-chains REVERT: A 316 ASP cc_start: 0.8402 (m-30) cc_final: 0.8153 (m-30) REVERT: A 463 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7473 (mtp180) REVERT: A 682 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: B 262 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7667 (tp) REVERT: B 316 ASP cc_start: 0.8397 (m-30) cc_final: 0.8154 (m-30) REVERT: B 463 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7472 (mtp180) REVERT: B 682 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7080 (tt0) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 1.1533 time to fit residues: 131.2440 Evaluate side-chains 111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11509 Z= 0.339 Angle : 0.566 13.072 15296 Z= 0.279 Chirality : 0.044 0.139 1744 Planarity : 0.005 0.040 1808 Dihedral : 8.209 58.709 2163 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.85 % Allowed : 11.46 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1352 helix: 0.92 (0.17), residues: 904 sheet: 2.99 (0.77), residues: 36 loop : -0.37 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 472 HIS 0.004 0.001 HIS A 640 PHE 0.018 0.002 PHE B 111 TYR 0.017 0.002 TYR B 16 ARG 0.003 0.000 ARG B 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.177 Fit side-chains REVERT: A 316 ASP cc_start: 0.8398 (m-30) cc_final: 0.8139 (m-30) REVERT: A 463 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7460 (mtp180) REVERT: A 682 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 262 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7700 (tp) REVERT: B 316 ASP cc_start: 0.8427 (m-30) cc_final: 0.8176 (m-30) REVERT: B 463 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7456 (mtp180) REVERT: B 682 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7106 (tt0) outliers start: 21 outliers final: 13 residues processed: 107 average time/residue: 1.1593 time to fit residues: 135.5004 Evaluate side-chains 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106106 restraints weight = 12584.840| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3192 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11509 Z= 0.188 Angle : 0.497 13.298 15296 Z= 0.243 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.038 1808 Dihedral : 7.549 59.250 2163 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.50 % Allowed : 12.08 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1352 helix: 1.11 (0.17), residues: 904 sheet: 3.13 (0.77), residues: 36 loop : -0.25 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.003 0.001 HIS A 640 PHE 0.012 0.001 PHE A 241 TYR 0.013 0.001 TYR A 16 ARG 0.001 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.28 seconds wall clock time: 66 minutes 33.03 seconds (3993.03 seconds total)