Starting phenix.real_space_refine on Sat Dec 9 14:56:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/12_2023/7lgw_23331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/12_2023/7lgw_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_23331/12_2023/7lgw_23331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/12_2023/7lgw_23331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/12_2023/7lgw_23331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/12_2023/7lgw_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.56, per 1000 atoms: 0.58 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: 4.55 Conformation dependent library (CDL) restraints added in 2.1 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: 2.52 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: 3.68 Time building geometry restraints manager: 4.82 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: 0.750 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: 4.230 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.510 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- 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 : 1.233 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 137 average time/residue: 1.2515 time to fit residues: 186.0858 Evaluate side-chains 100 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5686 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11509 Z= 0.255 Angle : 0.518 6.280 15296 Z= 0.259 Chirality : 0.042 0.129 1744 Planarity : 0.004 0.039 1808 Dihedral : 7.276 54.931 2163 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.32 % Allowed : 7.05 % Favored : 91.62 % 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: 1.28 (0.23), residues: 1352 helix: 1.29 (0.17), residues: 904 sheet: 3.11 (0.71), residues: 38 loop : -0.22 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 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 B 545 ARG 0.004 0.001 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 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.310 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 110 average time/residue: 1.2542 time to fit residues: 149.9718 Evaluate side-chains 103 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.3838 time to fit residues: 4.4814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.1117 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= 0.155 Angle : 0.451 7.630 15296 Z= 0.227 Chirality : 0.040 0.128 1744 Planarity : 0.004 0.035 1808 Dihedral : 6.858 57.464 2163 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.32 % Allowed : 8.73 % Favored : 89.95 % 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: 1.36 (0.23), residues: 1352 helix: 1.41 (0.17), residues: 906 sheet: 1.82 (0.72), residues: 50 loop : -0.30 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 PHE 0.020 0.001 PHE A 241 TYR 0.012 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 120 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.299 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 110 average time/residue: 1.2033 time to fit residues: 145.4661 Evaluate side-chains 99 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.6982 time to fit residues: 5.4098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11509 Z= 0.422 Angle : 0.612 9.530 15296 Z= 0.306 Chirality : 0.046 0.138 1744 Planarity : 0.005 0.052 1808 Dihedral : 8.768 59.759 2163 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.03 % Allowed : 10.67 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1352 helix: 0.94 (0.17), residues: 888 sheet: 2.79 (0.74), residues: 38 loop : -0.55 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 472 HIS 0.005 0.001 HIS B 640 PHE 0.020 0.002 PHE A 111 TYR 0.018 0.002 TYR B 16 ARG 0.003 0.001 ARG B 399 *********************** 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 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.202 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 114 average time/residue: 1.3459 time to fit residues: 166.8913 Evaluate side-chains 106 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 3 residues processed: 9 average time/residue: 0.5120 time to fit residues: 7.0657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11509 Z= 0.181 Angle : 0.490 10.007 15296 Z= 0.244 Chirality : 0.041 0.185 1744 Planarity : 0.004 0.037 1808 Dihedral : 7.787 57.532 2163 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.32 % Allowed : 11.99 % 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: 0.95 (0.23), residues: 1352 helix: 1.08 (0.17), residues: 904 sheet: 2.91 (0.73), residues: 38 loop : -0.49 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.002 0.001 HIS A 640 PHE 0.015 0.001 PHE A 269 TYR 0.013 0.001 TYR B 16 ARG 0.002 0.000 ARG B 31 *********************** 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 112 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.094 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 1.2388 time to fit residues: 144.3171 Evaluate side-chains 101 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1742 time to fit residues: 2.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11509 Z= 0.133 Angle : 0.457 9.388 15296 Z= 0.225 Chirality : 0.040 0.127 1744 Planarity : 0.003 0.035 1808 Dihedral : 6.916 58.719 2163 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 11.99 % 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: 1.27 (0.23), residues: 1352 helix: 1.32 (0.18), residues: 904 sheet: 3.23 (0.73), residues: 38 loop : -0.34 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.002 0.001 HIS A 220 PHE 0.016 0.001 PHE A 269 TYR 0.011 0.001 TYR B 16 ARG 0.003 0.000 ARG A 31 *********************** 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 111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.170 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 103 average time/residue: 1.0303 time to fit residues: 117.6741 Evaluate side-chains 96 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1056 time to fit residues: 2.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.0770 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11509 Z= 0.127 Angle : 0.465 12.377 15296 Z= 0.225 Chirality : 0.040 0.126 1744 Planarity : 0.003 0.035 1808 Dihedral : 6.544 59.024 2163 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.59 % Allowed : 12.17 % Favored : 86.24 % 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: 1.42 (0.23), residues: 1352 helix: 1.41 (0.18), residues: 906 sheet: 3.37 (0.72), residues: 38 loop : -0.24 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.002 0.001 HIS B 220 PHE 0.013 0.001 PHE B 269 TYR 0.011 0.001 TYR A 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 115 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.282 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 1.0939 time to fit residues: 126.4500 Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.2711 time to fit residues: 4.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 0.0060 chunk 125 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 overall best weight: 1.2138 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.1735 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= 0.152 Angle : 0.480 13.084 15296 Z= 0.231 Chirality : 0.040 0.133 1744 Planarity : 0.003 0.035 1808 Dihedral : 6.531 58.568 2163 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.59 % Allowed : 12.96 % Favored : 85.45 % 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: 1.43 (0.23), residues: 1352 helix: 1.39 (0.18), residues: 906 sheet: 3.39 (0.76), residues: 36 loop : -0.16 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS A 640 PHE 0.012 0.001 PHE A 241 TYR 0.012 0.001 TYR A 16 ARG 0.001 0.000 ARG B 31 *********************** 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 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.309 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 1.0511 time to fit residues: 121.9922 Evaluate side-chains 104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 6 average time/residue: 0.5726 time to fit residues: 5.6652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 454 GLN A 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11509 Z= 0.129 Angle : 0.461 13.052 15296 Z= 0.223 Chirality : 0.040 0.126 1744 Planarity : 0.003 0.035 1808 Dihedral : 6.313 59.228 2163 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.23 % Allowed : 13.49 % Favored : 85.27 % 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: 1.56 (0.23), residues: 1352 helix: 1.47 (0.18), residues: 908 sheet: 3.48 (0.75), residues: 36 loop : -0.08 (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 B 220 PHE 0.013 0.001 PHE B 269 TYR 0.011 0.001 TYR A 16 ARG 0.001 0.000 ARG A 399 *********************** 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 111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.223 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 1.0963 time to fit residues: 127.0304 Evaluate side-chains 101 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1496 time to fit residues: 2.8817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 454 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11509 Z= 0.462 Angle : 0.635 12.301 15296 Z= 0.314 Chirality : 0.047 0.194 1744 Planarity : 0.006 0.059 1808 Dihedral : 8.224 57.932 2163 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.23 % Allowed : 13.84 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1352 helix: 0.87 (0.17), residues: 904 sheet: 3.00 (0.78), residues: 36 loop : -0.46 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 699 HIS 0.006 0.001 HIS A 640 PHE 0.021 0.002 PHE A 111 TYR 0.020 0.002 TYR A 16 ARG 0.004 0.001 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 109 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.247 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 1.2608 time to fit residues: 144.4388 Evaluate side-chains 100 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1533 time to fit residues: 1.9304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 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 389 GLN A 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108967 restraints weight = 12537.773| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.82 r_work: 0.3213 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11509 Z= 0.148 Angle : 0.486 13.287 15296 Z= 0.236 Chirality : 0.041 0.132 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.098 59.567 2163 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.15 % Allowed : 13.76 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1352 helix: 1.19 (0.17), residues: 906 sheet: 3.09 (0.75), residues: 36 loop : -0.25 (0.31), residues: 410 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 0.012 0.001 PHE A 241 TYR 0.012 0.001 TYR A 16 ARG 0.002 0.000 ARG A 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.93 seconds wall clock time: 65 minutes 32.21 seconds (3932.21 seconds total)