Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:59:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/04_2022/7lgu_23329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/04_2022/7lgu_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_23329/04_2022/7lgu_23329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/04_2022/7lgu_23329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/04_2022/7lgu_23329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/04_2022/7lgu_23329_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: {'D10': 18, ' CL': 1, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25, 'CLR': 1, 'C14': 2} 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: {'D10': 18, ' CL': 1, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25, 'CLR': 1, 'C14': 2} 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: 7.31, per 1000 atoms: 0.63 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: 5.15 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: 1.32 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: 3.56 Time building geometry restraints manager: 5.50 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: 6365 17.99 - 35.98: 517 35.98 - 53.98: 92 53.98 - 71.97: 28 71.97 - 89.96: 12 Dihedral angle restraints: 7014 sinusoidal: 3090 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 7011 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 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. 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: 0.660 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: 4.760 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 34.300 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 14.183 89.961 4502 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 % 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 *********************** 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 : 1.397 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 1.0693 time to fit residues: 150.6495 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.7236 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 0.0980 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: 3.3786 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.0635 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= 0.277 Angle : 0.517 5.151 15392 Z= 0.265 Chirality : 0.044 0.150 1744 Planarity : 0.005 0.042 1808 Dihedral : 7.710 58.782 2132 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.09 % 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: 2.20 (0.69), residues: 50 loop : -0.24 (0.31), residues: 396 *********************** 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 154 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.277 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 138 average time/residue: 1.0894 time to fit residues: 165.2162 Evaluate side-chains 143 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 12 residues processed: 13 average time/residue: 0.7014 time to fit residues: 12.1255 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 0.0980 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8409 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 11620 Z= 0.146 Angle : 0.435 5.033 15392 Z= 0.223 Chirality : 0.041 0.131 1744 Planarity : 0.003 0.032 1808 Dihedral : 7.113 52.349 2132 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1352 helix: 1.46 (0.17), residues: 914 sheet: 2.34 (0.70), residues: 50 loop : -0.16 (0.31), residues: 388 *********************** 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 148 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.183 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 137 average time/residue: 1.0351 time to fit residues: 156.4146 Evaluate side-chains 137 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 9 average time/residue: 0.3161 time to fit residues: 5.4706 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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: 0.8458 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 11620 Z= 0.371 Angle : 0.554 5.188 15392 Z= 0.286 Chirality : 0.047 0.158 1744 Planarity : 0.005 0.051 1808 Dihedral : 8.503 51.660 2132 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 2.91 % 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: 1.09 (0.22), residues: 1352 helix: 1.16 (0.17), residues: 904 sheet: 3.24 (0.67), residues: 38 loop : -0.35 (0.29), residues: 410 *********************** 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 149 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.356 Fit side-chains outliers start: 33 outliers final: 22 residues processed: 135 average time/residue: 1.0501 time to fit residues: 156.3425 Evaluate side-chains 140 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.6030 time to fit residues: 9.3783 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.0781 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= 0.157 Angle : 0.445 5.023 15392 Z= 0.230 Chirality : 0.041 0.137 1744 Planarity : 0.004 0.035 1808 Dihedral : 7.705 51.525 2132 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.73 % 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: 1.34 (0.17), residues: 906 sheet: 2.35 (0.70), residues: 50 loop : -0.28 (0.31), residues: 396 *********************** 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 153 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.256 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 139 average time/residue: 1.0712 time to fit residues: 164.0656 Evaluate side-chains 135 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 9 average time/residue: 0.1895 time to fit residues: 4.4071 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 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 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 11620 Z= 0.351 Angle : 0.544 5.202 15392 Z= 0.281 Chirality : 0.046 0.155 1744 Planarity : 0.005 0.051 1808 Dihedral : 8.703 58.376 2132 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1352 helix: 1.13 (0.17), residues: 904 sheet: 3.22 (0.66), residues: 38 loop : -0.35 (0.29), residues: 410 *********************** 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: 32 poor density : 119 time to evaluate : 1.361 Fit side-chains outliers start: 32 outliers final: 21 residues processed: 136 average time/residue: 1.1107 time to fit residues: 166.0095 Evaluate side-chains 140 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.5132 time to fit residues: 7.8161 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 11620 Z= 0.158 Angle : 0.447 5.041 15392 Z= 0.231 Chirality : 0.041 0.142 1744 Planarity : 0.004 0.035 1808 Dihedral : 7.957 58.191 2132 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.59 % 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: 1.28 (0.23), residues: 1352 helix: 1.30 (0.17), residues: 910 sheet: 2.35 (0.70), residues: 50 loop : -0.29 (0.31), residues: 392 *********************** 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 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.405 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 137 average time/residue: 1.1763 time to fit residues: 176.7463 Evaluate side-chains 128 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2658 time to fit residues: 2.5756 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0987 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= 0.285 Angle : 0.511 5.155 15392 Z= 0.264 Chirality : 0.044 0.149 1744 Planarity : 0.005 0.042 1808 Dihedral : 8.561 58.363 2132 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.29 % 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 (0.22), residues: 1352 helix: 1.21 (0.17), residues: 904 sheet: 2.31 (0.70), residues: 50 loop : -0.30 (0.30), residues: 398 *********************** 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 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.402 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 1.1907 time to fit residues: 172.2517 Evaluate side-chains 135 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.6439 time to fit residues: 8.3032 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 11620 Z= 0.143 Angle : 0.442 5.037 15392 Z= 0.227 Chirality : 0.041 0.140 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.782 59.096 2132 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.97 % 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: 1.40 (0.23), residues: 1352 helix: 1.37 (0.17), residues: 916 sheet: 2.45 (0.70), residues: 50 loop : -0.22 (0.31), residues: 386 *********************** 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 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.353 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 126 average time/residue: 1.1355 time to fit residues: 156.9790 Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.9097 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.0995 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= 0.284 Angle : 0.516 5.150 15392 Z= 0.267 Chirality : 0.044 0.150 1744 Planarity : 0.005 0.042 1808 Dihedral : 8.347 56.273 2132 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1352 helix: 1.24 (0.17), residues: 906 sheet: 2.38 (0.73), residues: 48 loop : -0.20 (0.30), residues: 398 ********************** 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 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.376 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 1.2277 time to fit residues: 167.4275 Evaluate side-chains 122 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.8160 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095122 restraints weight = 12059.773| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.82 r_work: 0.3041 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.3010 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work: 0.2994 rms_B_bonded: 1.81 restraints_weight: 0.0625 r_work: 0.2977 rms_B_bonded: 1.98 restraints_weight: 0.0312 r_work: 0.2958 rms_B_bonded: 2.20 restraints_weight: 0.0156 r_work: 0.2938 rms_B_bonded: 2.46 restraints_weight: 0.0078 r_work: 0.2916 rms_B_bonded: 2.78 restraints_weight: 0.0039 r_work: 0.2891 rms_B_bonded: 3.17 restraints_weight: 0.0020 r_work: 0.2865 rms_B_bonded: 3.62 restraints_weight: 0.0010 r_work: 0.2836 rms_B_bonded: 4.16 restraints_weight: 0.0005 r_work: 0.2805 rms_B_bonded: 4.79 restraints_weight: 0.0002 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 11620 Z= 0.124 Angle : 0.430 4.998 15392 Z= 0.219 Chirality : 0.040 0.147 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.199 58.250 2132 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.88 % 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: 1.55 (0.23), residues: 1352 helix: 1.43 (0.17), residues: 922 sheet: 2.40 (0.73), residues: 48 loop : 0.01 (0.32), residues: 382 =============================================================================== Job complete usr+sys time: 3366.92 seconds wall clock time: 61 minutes 12.81 seconds (3672.81 seconds total)