Starting phenix.real_space_refine on Fri Mar 15 12:10:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/03_2024/7lgu_23329_updated.pdb" } resolution = 2.3 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= 0.006 sd= 0.048 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 7892 2.51 5 N 1690 2.21 5 O 1965 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 ARG 130": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B ASP 550": "OD1" <-> "OD2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B GLU 700": "OE1" <-> "OE2" Residue "B GLU 723": "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: 11597 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: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 517 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 18, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 517 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 18, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Time building chain proxies: 6.86, per 1000 atoms: 0.59 Number of scatterers: 11597 At special positions: 0 Unit cell: (102.16, 119.078, 113.222, 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 1965 8.00 N 1690 7.00 C 7892 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: 4.61 Conformation dependent library (CDL) restraints added in 1.7 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: 62 helices and 6 sheets defined 63.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.642A pdb=" N ARG A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.842A pdb=" N TRP A 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 104 removed outlier: 5.733A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.582A 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: 5.149A pdb=" N LYS A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.068A 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: 4.735A pdb=" N HIS A 337 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 340 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A 341 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 349 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 353 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 356 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 358 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.790A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.897A pdb=" N LYS A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLY A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.788A 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: 4.105A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 4.877A pdb=" N ASP A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 654 through 669 Processing helix chain 'A' and resid 681 through 689 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: 3.642A pdb=" N ARG B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.841A pdb=" N TRP B 70 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 104 removed outlier: 5.733A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.582A 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: 5.149A pdb=" N LYS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.069A 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: 4.736A pdb=" N HIS B 337 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR B 340 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL B 341 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 346 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 349 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 350 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 353 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 356 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 357 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 358 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.791A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.898A pdb=" N LYS B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY B 450 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N MET B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 4.788A 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: 4.106A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 559 removed outlier: 4.877A pdb=" N ASP B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 681 through 689 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: 4.544A 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: 6.668A pdb=" N THR A 641 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 538 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 643 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 540 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP A 645 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 673 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 644 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 6.433A 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: 4.544A 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: 6.668A pdb=" N THR B 641 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE B 538 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 643 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 540 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP B 645 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 673 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 644 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 6.433A 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 513 560 hydrogen bonds defined for protein. 1512 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: 2.79 Time building geometry restraints manager: 4.95 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: 3236 1.34 - 1.46: 1983 1.46 - 1.57: 6323 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11620 Sorted by residual: bond pdb=" C3 CLR A 802 " pdb=" O1 CLR A 802 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.06e+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 1.06e+00 bond pdb=" C21 HP6 B 841 " pdb=" C22 HP6 B 841 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.04e-01 bond pdb=" C8 D10 A 839 " pdb=" C9 D10 A 839 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 7.83e-01 bond pdb=" C2 D10 B 839 " pdb=" C3 D10 B 839 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 7.70e-01 ... (remaining 11615 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 336 106.75 - 113.57: 6794 113.57 - 120.38: 4107 120.38 - 127.20: 4055 127.20 - 134.01: 100 Bond angle restraints: 15392 Sorted by residual: angle pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " pdb=" CD GLU A 280 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.70e+00 3.46e-01 4.19e+00 angle pdb=" CB GLU B 280 " pdb=" CG GLU B 280 " pdb=" CD GLU B 280 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.70e+00 3.46e-01 4.08e+00 angle pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 117.33 119.26 -1.93 1.01e+00 9.80e-01 3.66e+00 angle pdb=" CA VAL B 107 " pdb=" C VAL B 107 " pdb=" N PRO B 108 " ideal model delta sigma weight residual 117.33 119.19 -1.86 1.01e+00 9.80e-01 3.39e+00 angle pdb=" C ARG B 463 " pdb=" N THR B 464 " pdb=" CA THR B 464 " ideal model delta sigma weight residual 122.60 119.32 3.28 1.88e+00 2.83e-01 3.04e+00 ... (remaining 15387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6475 17.99 - 35.98: 519 35.98 - 53.98: 92 53.98 - 71.97: 28 71.97 - 89.96: 12 Dihedral angle restraints: 7126 sinusoidal: 3202 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+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 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN A 548 " pdb=" C ASN A 548 " pdb=" N SER A 549 " pdb=" CA SER A 549 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 972 0.028 - 0.055: 458 0.055 - 0.083: 201 0.083 - 0.110: 93 0.110 - 0.138: 20 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 2.42 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA TYR B 526 " pdb=" N TYR B 526 " pdb=" C TYR B 526 " pdb=" CB TYR B 526 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA TYR A 526 " pdb=" N TYR A 526 " pdb=" C TYR A 526 " pdb=" CB TYR A 526 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1741 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 443 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ILE B 443 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE B 443 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL B 444 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 443 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ILE A 443 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE A 443 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 444 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 444 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C VAL A 444 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL A 444 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 445 " -0.007 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 813 2.74 - 3.28: 11324 3.28 - 3.82: 19601 3.82 - 4.36: 25256 4.36 - 4.90: 40665 Nonbonded interactions: 97659 Sorted by model distance: nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.197 2.440 nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 654 " pdb=" OE2 GLU B 468 " model vdw 2.259 2.440 nonbonded pdb=" OE2 GLU A 468 " pdb=" OG SER B 654 " model vdw 2.262 2.440 nonbonded pdb=" NE ARG B 211 " pdb=" OD2 ASP B 457 " model vdw 2.271 2.520 ... (remaining 97654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.290 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: 4.360 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.820 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 0.024 11620 Z= 0.188 Angle : 0.934 5.106 15392 Z= 0.377 Chirality : 0.042 0.138 1744 Planarity : 0.003 0.027 1808 Dihedral : 14.032 89.961 4614 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 14.02 % Favored : 84.83 % 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: 1.41 (0.23), residues: 1352 helix: 1.33 (0.17), residues: 898 sheet: 2.30 (0.71), residues: 50 loop : 0.01 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.013 0.001 PHE A 278 TYR 0.013 0.001 TYR A 16 ARG 0.002 0.000 ARG A 502 *********************** 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 131 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.223 Fit side-chains REVERT: A 207 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: A 686 ASP cc_start: 0.7967 (m-30) cc_final: 0.7765 (m-30) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 1.1277 time to fit residues: 157.8851 Evaluate side-chains 124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 529 VAL 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: 0.7980 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 0.0370 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 454 GLN A 638 ASN B 337 HIS B 454 GLN B 638 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11620 Z= 0.276 Angle : 0.513 5.136 15392 Z= 0.264 Chirality : 0.044 0.149 1744 Planarity : 0.005 0.042 1808 Dihedral : 8.390 80.790 2257 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.82 % Allowed : 13.32 % Favored : 83.86 % 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: 1.35 (0.23), residues: 1352 helix: 1.36 (0.17), residues: 906 sheet: 2.21 (0.69), residues: 50 loop : -0.24 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 PHE 0.018 0.002 PHE A 391 TYR 0.016 0.002 TYR A 16 ARG 0.002 0.000 ARG A 558 *********************** 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 152 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.098 Fit side-chains REVERT: A 207 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7002 (tm-30) outliers start: 32 outliers final: 23 residues processed: 136 average time/residue: 1.2064 time to fit residues: 179.1121 Evaluate side-chains 143 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11620 Z= 0.207 Angle : 0.465 5.079 15392 Z= 0.240 Chirality : 0.042 0.137 1744 Planarity : 0.004 0.034 1808 Dihedral : 8.162 58.759 2251 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.38 % Allowed : 14.11 % Favored : 83.51 % 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: 1.35 (0.17), residues: 910 sheet: 2.26 (0.70), residues: 50 loop : -0.20 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE B 391 TYR 0.013 0.001 TYR B 16 ARG 0.001 0.000 ARG B 20 *********************** 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 146 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.165 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 1.2078 time to fit residues: 172.4777 Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 chunk 109 optimal weight: 6.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11620 Z= 0.232 Angle : 0.483 5.111 15392 Z= 0.250 Chirality : 0.043 0.140 1744 Planarity : 0.004 0.038 1808 Dihedral : 8.319 59.794 2248 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.17 % Allowed : 13.40 % Favored : 83.42 % 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: 1.29 (0.23), residues: 1352 helix: 1.29 (0.17), residues: 910 sheet: 2.25 (0.69), residues: 50 loop : -0.21 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.004 0.001 HIS A 640 PHE 0.017 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG A 20 *********************** 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 155 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.233 Fit side-chains outliers start: 36 outliers final: 27 residues processed: 139 average time/residue: 1.1238 time to fit residues: 171.0268 Evaluate side-chains 146 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11620 Z= 0.208 Angle : 0.468 5.085 15392 Z= 0.241 Chirality : 0.042 0.137 1744 Planarity : 0.004 0.035 1808 Dihedral : 8.231 57.686 2248 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.35 % Allowed : 13.32 % Favored : 83.33 % 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: 1.32 (0.23), residues: 1352 helix: 1.32 (0.17), residues: 910 sheet: 2.30 (0.69), residues: 50 loop : -0.22 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE B 391 TYR 0.013 0.001 TYR B 16 ARG 0.002 0.000 ARG B 20 *********************** 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 158 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.199 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 139 average time/residue: 1.1261 time to fit residues: 171.4002 Evaluate side-chains 145 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11620 Z= 0.347 Angle : 0.543 5.190 15392 Z= 0.281 Chirality : 0.046 0.158 1744 Planarity : 0.005 0.049 1808 Dihedral : 9.254 59.835 2248 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.00 % Allowed : 14.20 % Favored : 82.80 % 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: 1.08 (0.22), residues: 1352 helix: 1.15 (0.17), residues: 904 sheet: 3.18 (0.66), residues: 38 loop : -0.36 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 70 HIS 0.005 0.001 HIS B 640 PHE 0.018 0.002 PHE B 391 TYR 0.016 0.002 TYR B 16 ARG 0.003 0.001 ARG A 20 *********************** 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 151 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.192 Fit side-chains REVERT: A 257 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7236 (pt) REVERT: A 285 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7160 (mtpp) REVERT: B 257 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7206 (pt) REVERT: B 285 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7159 (mtpp) REVERT: B 615 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6859 (ttpt) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 1.2388 time to fit residues: 183.1710 Evaluate side-chains 140 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11620 Z= 0.231 Angle : 0.484 5.105 15392 Z= 0.250 Chirality : 0.043 0.140 1744 Planarity : 0.004 0.036 1808 Dihedral : 8.930 58.473 2248 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.56 % Allowed : 14.64 % Favored : 82.80 % 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: 1.15 (0.22), residues: 1352 helix: 1.21 (0.17), residues: 904 sheet: 3.22 (0.66), residues: 38 loop : -0.35 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.004 0.001 HIS A 640 PHE 0.016 0.001 PHE A 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 20 *********************** 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 147 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.226 Fit side-chains REVERT: A 257 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7293 (pt) REVERT: A 285 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7180 (mtpp) REVERT: A 615 LYS cc_start: 0.7070 (ttpt) cc_final: 0.6852 (ttpt) REVERT: B 207 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: B 257 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7253 (pt) REVERT: B 615 LYS cc_start: 0.7076 (ttpt) cc_final: 0.6859 (ttpt) outliers start: 29 outliers final: 23 residues processed: 132 average time/residue: 1.2089 time to fit residues: 173.9397 Evaluate side-chains 144 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER 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: 9.9990 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11620 Z= 0.255 Angle : 0.496 5.154 15392 Z= 0.256 Chirality : 0.043 0.145 1744 Planarity : 0.004 0.040 1808 Dihedral : 8.884 56.334 2248 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.91 % Allowed : 14.46 % Favored : 82.63 % 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 (0.22), residues: 1352 helix: 1.19 (0.17), residues: 904 sheet: 2.33 (0.69), residues: 50 loop : -0.31 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.004 0.001 HIS A 640 PHE 0.016 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 20 *********************** 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 149 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.218 Fit side-chains REVERT: A 207 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 257 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7275 (pt) REVERT: A 285 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7181 (mtpp) REVERT: A 615 LYS cc_start: 0.7059 (ttpt) cc_final: 0.6838 (ttpt) REVERT: B 207 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: B 257 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7273 (pt) REVERT: B 615 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6850 (ttpt) outliers start: 33 outliers final: 23 residues processed: 132 average time/residue: 1.1993 time to fit residues: 172.3663 Evaluate side-chains 145 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11620 Z= 0.123 Angle : 0.428 5.028 15392 Z= 0.219 Chirality : 0.040 0.145 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.788 57.762 2248 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.76 % Allowed : 15.52 % Favored : 82.72 % 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: 1.61 (0.23), residues: 1352 helix: 1.49 (0.17), residues: 904 sheet: 2.43 (0.70), residues: 50 loop : 0.04 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 472 HIS 0.003 0.001 HIS B 220 PHE 0.010 0.001 PHE B 391 TYR 0.010 0.001 TYR B 16 ARG 0.002 0.000 ARG B 571 *********************** 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 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.235 Fit side-chains REVERT: A 615 LYS cc_start: 0.7101 (ttpt) cc_final: 0.6885 (ttpt) REVERT: B 207 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: B 615 LYS cc_start: 0.7106 (ttpt) cc_final: 0.6891 (ttpt) outliers start: 20 outliers final: 13 residues processed: 131 average time/residue: 1.2490 time to fit residues: 178.4551 Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11620 Z= 0.261 Angle : 0.497 5.159 15392 Z= 0.257 Chirality : 0.043 0.144 1744 Planarity : 0.004 0.038 1808 Dihedral : 8.333 55.535 2246 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 15.96 % Favored : 82.63 % 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: 1.29 (0.23), residues: 1352 helix: 1.29 (0.17), residues: 910 sheet: 2.40 (0.73), residues: 48 loop : -0.21 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.004 0.001 HIS A 640 PHE 0.017 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 20 ********************** 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 130 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.239 Fit side-chains REVERT: A 207 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 615 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6849 (ttpt) REVERT: B 207 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: B 615 LYS cc_start: 0.7093 (ttpt) cc_final: 0.6855 (ttpt) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 1.1718 time to fit residues: 154.9268 Evaluate side-chains 130 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.093779 restraints weight = 12041.795| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.82 r_work: 0.2926 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11620 Z= 0.134 Angle : 0.426 5.028 15392 Z= 0.219 Chirality : 0.040 0.143 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.514 56.805 2246 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.41 % Allowed : 16.05 % Favored : 82.54 % 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: 1.68 (0.23), residues: 1352 helix: 1.52 (0.17), residues: 906 sheet: 2.46 (0.73), residues: 48 loop : 0.15 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.003 0.001 HIS B 220 PHE 0.009 0.001 PHE B 391 TYR 0.010 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: 3950.86 seconds wall clock time: 71 minutes 11.39 seconds (4271.39 seconds total)