Starting phenix.real_space_refine (version: dev) on Mon Feb 20 05:17:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxg_24730/02_2023/7rxg_24730_updated.pdb" } resolution = 2.28 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= -0.000 sd= 0.004 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 "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 704": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 714": "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: 11380 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5258 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5258 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 326 Unusual residues: {' CA': 2, 'PGW': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-2': 1, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 394 Unusual residues: {' CA': 2, 'PGW': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-2': 1, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 72 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 72 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 6.79, per 1000 atoms: 0.60 Number of scatterers: 11380 At special positions: 0 Unit cell: (86.9241, 127.913, 100.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 20 15.00 O 2082 8.00 N 1766 7.00 C 7374 6.00 H 96 1.00 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: 5.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 66.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'B' and resid 29 through 45 Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 145 through 157 removed outlier: 4.178A pdb=" N LYS B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 175 through 204 removed outlier: 3.697A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 210 through 237 Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 273 through 310 removed outlier: 4.355A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix Processing helix chain 'B' and resid 318 through 349 removed outlier: 4.461A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 383 removed outlier: 3.980A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 393 through 402 removed outlier: 4.124A pdb=" N ASP B 397 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 398 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 401 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 436 through 462 removed outlier: 4.735A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 491 through 502 removed outlier: 3.656A pdb=" N GLU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 528 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.787A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 590 removed outlier: 4.376A pdb=" N SER B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 3.527A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'B' and resid 703 through 706 No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'A' and resid 29 through 45 Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 145 through 157 removed outlier: 4.178A pdb=" N LYS A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 204 removed outlier: 3.697A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 210 through 237 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 273 through 310 removed outlier: 4.355A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 318 through 349 removed outlier: 4.462A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.980A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 393 through 402 removed outlier: 4.124A pdb=" N ASP A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 398 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 436 through 462 removed outlier: 4.735A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.656A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 528 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.787A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 removed outlier: 4.376A pdb=" N SER A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.527A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 657 Processing helix chain 'A' and resid 703 through 706 No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 712 through 723 Processing sheet with id= A, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.594A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE B 61 " --> pdb=" O GLN B 54 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN B 54 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 63 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B 52 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG B 65 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR B 50 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.594A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE A 61 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN A 54 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE A 63 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL A 52 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 65 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR A 50 " --> pdb=" O ARG A 65 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1698 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: 3.61 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 96 1.03 - 1.22: 46 1.22 - 1.42: 4769 1.42 - 1.61: 6579 1.61 - 1.81: 96 Bond restraints: 11586 Sorted by residual: bond pdb=" C1 PGW B 809 " pdb=" O01 PGW B 809 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C1 PGW A1112 " pdb=" O01 PGW A1112 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 PGW A1109 " pdb=" O01 PGW A1109 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C1 PGW B 806 " pdb=" O01 PGW B 806 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A1111 " pdb=" O01 PGW A1111 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 11581 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 343 106.77 - 113.58: 6526 113.58 - 120.40: 4582 120.40 - 127.22: 3945 127.22 - 134.03: 134 Bond angle restraints: 15530 Sorted by residual: angle pdb=" CA PHE B 419 " pdb=" C PHE B 419 " pdb=" O PHE B 419 " ideal model delta sigma weight residual 120.82 113.55 7.27 1.05e+00 9.07e-01 4.79e+01 angle pdb=" CA PHE A 419 " pdb=" C PHE A 419 " pdb=" O PHE A 419 " ideal model delta sigma weight residual 120.82 113.63 7.19 1.05e+00 9.07e-01 4.69e+01 angle pdb=" O PHE B 419 " pdb=" C PHE B 419 " pdb=" N SER B 420 " ideal model delta sigma weight residual 122.07 127.32 -5.25 1.03e+00 9.43e-01 2.60e+01 angle pdb=" O PHE A 419 " pdb=" C PHE A 419 " pdb=" N SER A 420 " ideal model delta sigma weight residual 122.07 127.24 -5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" N VAL A 403 " pdb=" CA VAL A 403 " pdb=" C VAL A 403 " ideal model delta sigma weight residual 112.80 108.35 4.45 1.15e+00 7.56e-01 1.50e+01 ... (remaining 15525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 6488 32.34 - 64.68: 268 64.68 - 97.02: 30 97.02 - 129.36: 4 129.36 - 161.70: 4 Dihedral angle restraints: 6794 sinusoidal: 2960 harmonic: 3834 Sorted by residual: dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ALA B 389 " pdb=" C ALA B 389 " pdb=" N SER B 390 " pdb=" CA SER B 390 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C01 PGW A1113 " pdb=" C19 PGW A1113 " pdb=" O03 PGW A1113 " pdb=" O04 PGW A1113 " ideal model delta sinusoidal sigma weight residual 9.00 -152.70 161.70 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1021 0.038 - 0.075: 468 0.075 - 0.113: 127 0.113 - 0.151: 32 0.151 - 0.189: 22 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CA GLU B 418 " pdb=" N GLU B 418 " pdb=" C GLU B 418 " pdb=" CB GLU B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA GLU A 418 " pdb=" N GLU A 418 " pdb=" C GLU A 418 " pdb=" CB GLU A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" C02 PGW A1102 " pdb=" C01 PGW A1102 " pdb=" C03 PGW A1102 " pdb=" O01 PGW A1102 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 1667 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 420 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C SER B 420 " 0.059 2.00e-02 2.50e+03 pdb=" O SER B 420 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 421 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 420 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER A 420 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 420 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 421 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 404 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C ARG A 404 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 404 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 405 " -0.016 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 62 2.30 - 2.87: 4121 2.87 - 3.45: 13798 3.45 - 4.02: 23965 4.02 - 4.60: 35277 Nonbonded interactions: 77223 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" H1 HOH A2702 " model vdw 1.722 1.850 nonbonded pdb=" OG SER B 546 " pdb=" H1 HOH B2702 " model vdw 1.722 1.850 nonbonded pdb=" O LYS B 556 " pdb=" H1 HOH B2709 " model vdw 1.739 1.850 nonbonded pdb=" O LYS A 556 " pdb=" H1 HOH A2709 " model vdw 1.739 1.850 nonbonded pdb=" OH TYR A 621 " pdb=" H1 HOH A2705 " model vdw 1.739 1.850 ... (remaining 77218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 724 or (resid 1105 and (name C01 or name C02 or \ name C03 or name C1 or name C10 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or na \ me C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O01 or name O02 or name O03 or name O04 or name O11)) or (resid 1106 and (name \ C01 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or nam \ e C21 or name C22 or name O01 or name O02 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )) or (resid 1107 and (name C01 or n \ ame C02 or name C03 or name C19 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name O01 or name O02 or name O03 or name O11 or \ name O12 or name O13 or name O14 or name P )) or (resid 1108 and (name C01 or na \ me C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name \ C30 or name C4 )) or (resid 1109 and (name C01 or name C02 or name C03 or name C \ 3 or name C4 or name C5 or name C6 or name O01 or name O02 or name O03 or name O \ 04 or name O11 or name O12 or name O13 or name O14 or name P )) or (resid 1110 a \ nd (name C01 or name C02 or name C03 or name C3 or name C4 or name C5 or name C6 \ or name C7 or name O01 or name O02 or name O03 or name O11 or name O12 or name \ O13 or name O14 or name P )) or (resid 1111 and (name C01 or name C02 or name C0 \ 3 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or \ name O13 or name O14 or name P )) or resid 1112)) selection = (chain 'B' and (resid 12 through 724 or (resid 805 and (name C01 or name C02 or \ name C03 or name C1 or name C10 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ e C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O01 or name O02 or name O03 or name O04 or name O11)) or (resid 806 and (name C0 \ 1 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name \ C21 or name C22 or name O01 or name O02 or name O03 or name O04 or name O11 or n \ ame O12 or name O13 or name O14 or name P )) or (resid 807 and (name C01 or name \ C02 or name C03 or name C19 or name C2 or name C3 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name O01 or name O02 or name O03 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or (resid 808 and (name C01 or name C \ 02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 \ or name C4 )) or (resid 809 and (name C01 or name C02 or name C03 or name C3 or \ name C4 or name C5 or name C6 or name O01 or name O02 or name O03 or name O04 or \ name O11 or name O12 or name O13 or name O14 or name P )) or (resid 810 and (na \ me C01 or name C02 or name C03 or name C3 or name C4 or name C5 or name C6 or na \ me C7 or name O01 or name O02 or name O03 or name O11 or name O12 or name O13 or \ name O14 or name P )) or (resid 811 and (name C01 or name C02 or name C03 or na \ me C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )) or (resid 812 and (name C01 or name C02 or name C03 o \ r name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C \ 5 or name C6 or name O01 or name O02 or name O03 or name O04 or name O11 or name \ O12 or name O13 or name O14 or name P )))) } 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 20 5.49 5 S 38 5.16 5 C 7374 2.51 5 N 1766 2.21 5 O 2082 1.98 5 H 96 0.53 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: 3.160 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: 0.380 Extract box with map and model: 12.960 Check model and map are aligned: 0.180 Process input model: 32.750 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.008 0.094 11490 Z= 0.505 Angle : 1.269 11.455 15482 Z= 0.549 Chirality : 0.049 0.189 1670 Planarity : 0.005 0.045 1902 Dihedral : 17.948 161.703 4306 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer Outliers : 0.18 % 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: -0.83 (0.21), residues: 1288 helix: 0.09 (0.16), residues: 884 sheet: -0.80 (0.56), residues: 54 loop : -1.95 (0.31), residues: 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.312 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 1.6980 time to fit residues: 328.3502 Evaluate side-chains 130 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 78 GLN B 113 HIS B 148 ASN B 150 GLN B 171 ASN B 283 GLN B 355 GLN B 370 ASN B 400 HIS B 438 GLN B 453 GLN B 593 ASN B 599 ASN B 639 ASN A 58 ASN A 78 GLN A 113 HIS A 148 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 283 GLN A 355 GLN A 370 ASN A 400 HIS A 438 GLN A 453 GLN A 593 ASN A 599 ASN A 639 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11490 Z= 0.281 Angle : 0.604 5.405 15482 Z= 0.326 Chirality : 0.044 0.198 1670 Planarity : 0.006 0.041 1902 Dihedral : 17.103 148.682 1860 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.23 % 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: 0.59 (0.23), residues: 1288 helix: 1.19 (0.17), residues: 888 sheet: 0.48 (0.63), residues: 44 loop : -1.64 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 144 average time/residue: 1.6410 time to fit residues: 251.9570 Evaluate side-chains 142 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.8234 time to fit residues: 5.5261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11490 Z= 0.191 Angle : 0.495 4.626 15482 Z= 0.272 Chirality : 0.040 0.173 1670 Planarity : 0.004 0.036 1902 Dihedral : 15.099 131.630 1860 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.79 % 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 (0.24), residues: 1288 helix: 1.69 (0.17), residues: 888 sheet: 1.05 (0.67), residues: 44 loop : -1.34 (0.34), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 145 average time/residue: 1.7436 time to fit residues: 268.9481 Evaluate side-chains 143 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.5419 time to fit residues: 6.1653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 11490 Z= 0.230 Angle : 0.539 4.756 15482 Z= 0.294 Chirality : 0.041 0.184 1670 Planarity : 0.005 0.042 1902 Dihedral : 14.549 125.552 1860 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.59 % 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: 1.41 (0.24), residues: 1288 helix: 1.77 (0.17), residues: 888 sheet: 0.60 (0.72), residues: 48 loop : -1.21 (0.35), residues: 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.358 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 147 average time/residue: 1.6556 time to fit residues: 260.5760 Evaluate side-chains 147 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 4 residues processed: 9 average time/residue: 0.5631 time to fit residues: 8.0615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 11490 Z= 0.397 Angle : 0.699 5.985 15482 Z= 0.373 Chirality : 0.049 0.231 1670 Planarity : 0.007 0.085 1902 Dihedral : 15.442 132.668 1860 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1288 helix: 1.50 (0.17), residues: 886 sheet: 0.66 (0.73), residues: 48 loop : -1.30 (0.35), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.440 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 151 average time/residue: 1.6861 time to fit residues: 271.5771 Evaluate side-chains 144 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.1840 time to fit residues: 3.8734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11490 Z= 0.173 Angle : 0.492 4.608 15482 Z= 0.270 Chirality : 0.039 0.177 1670 Planarity : 0.004 0.038 1902 Dihedral : 14.206 123.141 1860 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.05 % 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: 1.48 (0.24), residues: 1288 helix: 1.85 (0.17), residues: 884 sheet: 0.79 (0.74), residues: 48 loop : -1.25 (0.35), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.546 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 144 average time/residue: 1.8301 time to fit residues: 279.9006 Evaluate side-chains 146 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.6466 time to fit residues: 6.4237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11490 Z= 0.206 Angle : 0.518 4.777 15482 Z= 0.283 Chirality : 0.040 0.179 1670 Planarity : 0.005 0.039 1902 Dihedral : 13.692 105.996 1860 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.43 % 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 (0.24), residues: 1288 helix: 1.86 (0.17), residues: 886 sheet: 0.91 (0.75), residues: 48 loop : -1.24 (0.35), residues: 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.431 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 144 average time/residue: 1.8266 time to fit residues: 279.6211 Evaluate side-chains 145 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6774 time to fit residues: 4.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 15 HIS A 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11490 Z= 0.230 Angle : 0.543 4.859 15482 Z= 0.295 Chirality : 0.041 0.185 1670 Planarity : 0.005 0.038 1902 Dihedral : 13.625 83.836 1860 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.61 % 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: 1.47 (0.24), residues: 1288 helix: 1.82 (0.17), residues: 886 sheet: 0.94 (0.75), residues: 48 loop : -1.23 (0.35), residues: 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.487 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 1.7694 time to fit residues: 269.0885 Evaluate side-chains 148 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.4860 time to fit residues: 6.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS B 58 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 11490 Z= 0.341 Angle : 0.652 5.813 15482 Z= 0.349 Chirality : 0.046 0.215 1670 Planarity : 0.006 0.050 1902 Dihedral : 14.365 87.093 1860 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.34 % 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 (0.24), residues: 1288 helix: 1.63 (0.17), residues: 886 sheet: 0.86 (0.74), residues: 48 loop : -1.28 (0.35), residues: 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.307 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 148 average time/residue: 1.7292 time to fit residues: 272.0744 Evaluate side-chains 142 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.1920 time to fit residues: 3.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 11490 Z= 0.335 Angle : 0.644 5.854 15482 Z= 0.344 Chirality : 0.046 0.211 1670 Planarity : 0.006 0.071 1902 Dihedral : 14.700 89.932 1860 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.71 % 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: 1.23 (0.24), residues: 1288 helix: 1.59 (0.17), residues: 884 sheet: 1.48 (0.73), residues: 44 loop : -1.22 (0.35), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.350 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 147 average time/residue: 1.8063 time to fit residues: 283.5796 Evaluate side-chains 147 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1838 time to fit residues: 2.7658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN A 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114091 restraints weight = 9718.466| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.05 r_work: 0.3010 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 11490 Z= 0.286 Angle : 0.598 5.581 15482 Z= 0.323 Chirality : 0.044 0.200 1670 Planarity : 0.005 0.040 1902 Dihedral : 14.538 90.356 1860 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.98 % 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: 1.26 (0.24), residues: 1288 helix: 1.63 (0.17), residues: 886 sheet: 0.84 (0.73), residues: 48 loop : -1.20 (0.36), residues: 354 =============================================================================== Job complete usr+sys time: 4901.99 seconds wall clock time: 88 minutes 14.65 seconds (5294.65 seconds total)