Starting phenix.real_space_refine (version: dev) on Mon Feb 20 07:11:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/02_2023/7lgu_23329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/02_2023/7lgu_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_23329/02_2023/7lgu_23329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/02_2023/7lgu_23329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/02_2023/7lgu_23329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgu_23329/02_2023/7lgu_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 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-4877/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: 7.08, per 1000 atoms: 0.61 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: 4.65 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: 1.43 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: 3.44 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: 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.180 Process input model: 32.650 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.770 ------------------------------------------------------------------------------- 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 : 1.337 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 1.1172 time to fit residues: 156.8011 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.7947 ------------------------------------------------------------------------------- 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 58.781 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 : 1.396 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 138 average time/residue: 1.1966 time to fit residues: 181.0183 Evaluate side-chains 143 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 12 residues processed: 13 average time/residue: 0.5992 time to fit residues: 10.5915 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11620 Z= 0.171 Angle : 0.449 5.050 15392 Z= 0.231 Chirality : 0.041 0.132 1744 Planarity : 0.004 0.033 1808 Dihedral : 7.340 52.192 2132 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 1.42 (0.23), residues: 1352 helix: 1.42 (0.17), residues: 908 sheet: 2.29 (0.70), residues: 50 loop : -0.23 (0.31), residues: 394 *********************** 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 151 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.287 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 138 average time/residue: 1.1733 time to fit residues: 177.1509 Evaluate side-chains 137 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 10 residues processed: 10 average time/residue: 0.3097 time to fit residues: 5.5797 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 109 optimal weight: 10.0000 overall best weight: 3.3704 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.0827 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 : 0.509 5.158 15392 Z= 0.263 Chirality : 0.044 0.146 1744 Planarity : 0.005 0.041 1808 Dihedral : 8.099 50.922 2132 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1352 helix: 1.26 (0.17), residues: 906 sheet: 3.23 (0.65), residues: 38 loop : -0.27 (0.30), residues: 408 *********************** 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 152 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.178 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 137 average time/residue: 1.1831 time to fit residues: 177.4575 Evaluate side-chains 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 12 residues processed: 11 average time/residue: 0.6153 time to fit residues: 9.7335 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.0776 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= 0.163 Angle : 0.446 5.058 15392 Z= 0.230 Chirality : 0.041 0.134 1744 Planarity : 0.004 0.034 1808 Dihedral : 7.535 50.670 2132 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.47 % 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: 1.40 (0.17), residues: 906 sheet: 2.32 (0.70), residues: 50 loop : -0.24 (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 146 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.557 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 133 average time/residue: 1.1584 time to fit residues: 168.7655 Evaluate side-chains 134 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 10 residues processed: 9 average time/residue: 0.1730 time to fit residues: 4.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 0.1980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.0827 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= 0.183 Angle : 0.454 5.083 15392 Z= 0.234 Chirality : 0.041 0.135 1744 Planarity : 0.004 0.035 1808 Dihedral : 7.478 52.613 2132 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.20 % 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: 1.39 (0.23), residues: 1352 helix: 1.39 (0.17), residues: 910 sheet: 2.34 (0.70), residues: 50 loop : -0.26 (0.31), residues: 392 *********************** 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 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.185 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 133 average time/residue: 1.2094 time to fit residues: 176.3646 Evaluate side-chains 137 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.8378 time to fit residues: 9.3134 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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: 0.8455 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 11620 Z= 0.332 Angle : 0.538 5.183 15392 Z= 0.278 Chirality : 0.046 0.158 1744 Planarity : 0.005 0.047 1808 Dihedral : 8.654 59.994 2132 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.12 (0.22), residues: 1352 helix: 1.17 (0.17), residues: 904 sheet: 3.24 (0.67), residues: 38 loop : -0.35 (0.29), residues: 410 *********************** 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 150 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.243 Fit side-chains outliers start: 31 outliers final: 21 residues processed: 135 average time/residue: 1.2171 time to fit residues: 179.2849 Evaluate side-chains 136 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.4838 time to fit residues: 7.4225 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8459 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 11620 Z= 0.340 Angle : 0.544 5.204 15392 Z= 0.281 Chirality : 0.046 0.160 1744 Planarity : 0.005 0.047 1808 Dihedral : 9.250 55.192 2132 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1352 helix: 1.06 (0.17), residues: 904 sheet: 3.17 (0.70), residues: 36 loop : -0.33 (0.29), residues: 412 *********************** 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 140 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.536 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 136 average time/residue: 1.2679 time to fit residues: 188.0331 Evaluate side-chains 130 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2618 time to fit residues: 2.5478 ------------------------------------------------------------------------------- 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: 1.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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: 0.8403 moved from start: 0.0963 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= 0.137 Angle : 0.440 5.020 15392 Z= 0.225 Chirality : 0.041 0.146 1744 Planarity : 0.003 0.035 1808 Dihedral : 7.893 56.596 2132 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.32 % 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: 1.37 (0.23), residues: 1352 helix: 1.34 (0.17), residues: 916 sheet: 2.33 (0.72), residues: 48 loop : -0.19 (0.31), residues: 388 *********************** 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 136 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.352 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 1.1858 time to fit residues: 173.9945 Evaluate side-chains 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.7233 time to fit residues: 5.4638 ------------------------------------------------------------------------------- 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: 0.8980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 0.0570 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 11620 Z= 0.172 Angle : 0.455 5.098 15392 Z= 0.234 Chirality : 0.041 0.136 1744 Planarity : 0.004 0.035 1808 Dihedral : 7.691 56.432 2132 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 1.36 (0.17), residues: 918 sheet: 2.37 (0.73), residues: 48 loop : -0.14 (0.31), residues: 386 ********************** 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 129 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.426 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 1.2388 time to fit residues: 173.3858 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1129 time to fit residues: 1.9306 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.131506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091340 restraints weight = 12029.834| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.81 r_work: 0.2887 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 11620 Z= 0.196 Angle : 0.472 5.116 15392 Z= 0.242 Chirality : 0.042 0.135 1744 Planarity : 0.004 0.036 1808 Dihedral : 7.748 55.655 2132 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.34 (0.23), residues: 1352 helix: 1.34 (0.17), residues: 912 sheet: 2.28 (0.73), residues: 48 loop : -0.23 (0.31), residues: 392 =============================================================================== Job complete usr+sys time: 3823.71 seconds wall clock time: 69 minutes 33.32 seconds (4173.32 seconds total)