Starting phenix.real_space_refine on Mon Mar 18 14:14:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm6_22386/03_2024/7jm6_22386_trim_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.427 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 64 5.16 5 Cl 6 4.86 5 C 6810 2.51 5 N 1744 2.21 5 O 1944 1.98 5 H 10504 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 95": "OD1" <-> "OD2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 706": "OD1" <-> "OD2" Residue "A ARG 713": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 746": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 752": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 758": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 782": "OD1" <-> "OD2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 706": "OD1" <-> "OD2" Residue "B ARG 713": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 746": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 752": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 758": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 782": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21084 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 10426 Classifications: {'peptide': 667} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 639} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 10426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 10426 Classifications: {'peptide': 667} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 639} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 9.88, per 1000 atoms: 0.47 Number of scatterers: 21084 At special positions: 0 Unit cell: (85.784, 116.523, 101.511, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 6 17.00 S 64 16.00 P 10 15.00 Mg 2 11.99 O 1944 8.00 N 1744 7.00 C 6810 6.00 H 10504 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: 18.63 Conformation dependent library (CDL) restraints added in 2.3 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 60.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 117 through 164 removed outlier: 4.533A pdb=" N ASP A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 192 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.010A pdb=" N ILE A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 257 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 316 through 341 Processing helix chain 'A' and resid 367 through 401 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 405 through 430 Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 509 through 530 Processing helix chain 'A' and resid 539 through 554 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 573 through 592 removed outlier: 3.610A pdb=" N PHE A 576 " --> pdb=" O THR A 573 " (cutoff:3.500A) Proline residue: A 577 - end of helix removed outlier: 3.702A pdb=" N VAL A 581 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 588 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 590 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 677 through 685 Processing helix chain 'A' and resid 704 through 710 removed outlier: 3.977A pdb=" N ALA A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 117 through 164 removed outlier: 4.533A pdb=" N ASP B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 192 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.009A pdb=" N ILE B 256 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 257 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 299 through 310 Processing helix chain 'B' and resid 316 through 341 Processing helix chain 'B' and resid 367 through 401 Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 405 through 430 Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 509 through 530 Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 573 through 592 removed outlier: 3.609A pdb=" N PHE B 576 " --> pdb=" O THR B 573 " (cutoff:3.500A) Proline residue: B 577 - end of helix removed outlier: 3.702A pdb=" N VAL B 581 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 585 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 588 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 590 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 604 Processing helix chain 'B' and resid 622 through 625 No H-bonds generated for 'chain 'B' and resid 622 through 625' Processing helix chain 'B' and resid 639 through 647 Processing helix chain 'B' and resid 677 through 685 Processing helix chain 'B' and resid 704 through 710 removed outlier: 3.977A pdb=" N ALA B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 780 through 784 Processing sheet with id= A, first strand: chain 'A' and resid 636 through 638 Processing sheet with id= B, first strand: chain 'A' and resid 743 through 745 removed outlier: 6.404A pdb=" N VAL A 766 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 655 through 659 Processing sheet with id= D, first strand: chain 'B' and resid 636 through 638 Processing sheet with id= E, first strand: chain 'B' and resid 743 through 745 removed outlier: 6.406A pdb=" N VAL B 766 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 655 through 659 590 hydrogen bonds defined for protein. 1644 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: 7.93 Time building geometry restraints manager: 19.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10486 1.03 - 1.23: 40 1.23 - 1.42: 4450 1.42 - 1.62: 6158 1.62 - 1.81: 116 Bond restraints: 21250 Sorted by residual: bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C5 ATP B 901 " pdb=" C6 ATP B 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C8 ATP A 901 " pdb=" N7 ATP A 901 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 21245 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.64: 374 106.64 - 114.19: 25485 114.19 - 121.73: 8861 121.73 - 129.27: 3578 129.27 - 136.81: 76 Bond angle restraints: 38374 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.20 18.67 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 121.26 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 120.40 16.43 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 120.43 16.40 1.00e+00 1.00e+00 2.69e+02 angle pdb=" C5 ATP B 901 " pdb=" C4 ATP B 901 " pdb=" N3 ATP B 901 " ideal model delta sigma weight residual 126.80 119.28 7.52 1.00e+00 1.00e+00 5.65e+01 ... (remaining 38369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.10: 9464 24.10 - 48.20: 382 48.20 - 72.31: 162 72.31 - 96.41: 16 96.41 - 120.51: 4 Dihedral angle restraints: 10028 sinusoidal: 5414 harmonic: 4614 Sorted by residual: dihedral pdb=" CA ILE A 213 " pdb=" C ILE A 213 " pdb=" N PRO A 214 " pdb=" CA PRO A 214 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ILE B 213 " pdb=" C ILE B 213 " pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C22 0J1 B 906 " pdb=" C24 0J1 B 906 " pdb=" C26 0J1 B 906 " pdb=" C28 0J1 B 906 " ideal model delta sinusoidal sigma weight residual -52.95 67.56 -120.51 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 10025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.996: 1680 0.996 - 1.992: 0 1.992 - 2.989: 0 2.989 - 3.985: 0 3.985 - 4.981: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C24 0J1 B 906 " pdb=" C22 0J1 B 906 " pdb=" C26 0J1 B 906 " pdb=" O25 0J1 B 906 " both_signs ideal model delta sigma weight residual False -2.51 2.47 -4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C24 0J1 A 906 " pdb=" C22 0J1 A 906 " pdb=" C26 0J1 A 906 " pdb=" O25 0J1 A 906 " both_signs ideal model delta sigma weight residual False -2.51 2.47 -4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1679 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 364 " 0.027 2.00e-02 2.50e+03 5.41e-02 2.93e+01 pdb=" C GLY A 364 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 364 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR A 365 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 364 " -0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C GLY B 364 " 0.093 2.00e-02 2.50e+03 pdb=" O GLY B 364 " -0.035 2.00e-02 2.50e+03 pdb=" N TYR B 365 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 191 " -0.019 2.00e-02 2.50e+03 1.53e-02 7.00e+00 pdb=" CG PHE B 191 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 191 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 191 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 191 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 191 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 191 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 191 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 191 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 191 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 191 " 0.001 2.00e-02 2.50e+03 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 189 2.05 - 2.68: 32387 2.68 - 3.32: 64574 3.32 - 3.96: 83091 3.96 - 4.60: 131029 Nonbonded interactions: 311270 Sorted by model distance: nonbonded pdb="HH12 ARG A 752 " pdb=" O SER B 740 " model vdw 1.408 1.850 nonbonded pdb=" O SER A 740 " pdb="HH12 ARG B 752 " model vdw 1.411 1.850 nonbonded pdb=" O MET A 363 " pdb=" HH TYR A 574 " model vdw 1.589 1.850 nonbonded pdb=" O MET B 363 " pdb=" HH TYR B 574 " model vdw 1.589 1.850 nonbonded pdb=" O SER A 86 " pdb=" HZ1 LYS A 781 " model vdw 1.616 1.850 ... (remaining 311265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.340 Extract box with map and model: 12.820 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 72.140 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.005 0.096 10746 Z= 0.341 Angle : 0.786 18.667 14596 Z= 0.532 Chirality : 0.177 4.981 1682 Planarity : 0.005 0.054 1804 Dihedral : 14.549 120.512 3884 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.72 % Allowed : 0.36 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.30 (0.22), residues: 1322 helix: 1.80 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 519 HIS 0.017 0.002 HIS B 403 PHE 0.045 0.002 PHE B 191 TYR 0.009 0.001 TYR A 365 ARG 0.005 0.001 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6363 (mtm-85) REVERT: B 108 ARG cc_start: 0.6624 (mtm110) cc_final: 0.6389 (mtm-85) REVERT: B 376 MET cc_start: 0.8853 (mtm) cc_final: 0.8612 (mtm) outliers start: 8 outliers final: 0 residues processed: 186 average time/residue: 2.1087 time to fit residues: 431.6605 Evaluate side-chains 150 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10746 Z= 0.324 Angle : 0.574 7.160 14596 Z= 0.302 Chirality : 0.044 0.276 1682 Planarity : 0.005 0.035 1804 Dihedral : 10.655 81.987 1556 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.53 % Allowed : 6.82 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.22), residues: 1322 helix: 1.97 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -0.78 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 519 HIS 0.003 0.001 HIS B 600 PHE 0.022 0.002 PHE A 324 TYR 0.010 0.001 TYR B 542 ARG 0.003 0.000 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 ARG cc_start: 0.7254 (ttp-170) cc_final: 0.6970 (ttm110) REVERT: B 490 LEU cc_start: 0.7348 (tt) cc_final: 0.7089 (mt) outliers start: 17 outliers final: 10 residues processed: 168 average time/residue: 2.3020 time to fit residues: 422.7205 Evaluate side-chains 168 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10746 Z= 0.228 Angle : 0.497 6.975 14596 Z= 0.263 Chirality : 0.039 0.212 1682 Planarity : 0.005 0.039 1804 Dihedral : 10.278 86.356 1556 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.62 % Allowed : 8.89 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.60 (0.23), residues: 1322 helix: 2.06 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.73 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 519 HIS 0.002 0.001 HIS B 653 PHE 0.015 0.001 PHE A 324 TYR 0.007 0.001 TYR A 392 ARG 0.004 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 ARG cc_start: 0.7261 (ttp-170) cc_final: 0.7032 (ttm110) REVERT: B 269 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7428 (mmtt) REVERT: B 309 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8020 (mp0) REVERT: B 490 LEU cc_start: 0.7451 (tt) cc_final: 0.7152 (mt) REVERT: B 747 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6930 (mp0) outliers start: 18 outliers final: 9 residues processed: 183 average time/residue: 2.2283 time to fit residues: 447.6592 Evaluate side-chains 173 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10746 Z= 0.190 Angle : 0.482 7.253 14596 Z= 0.253 Chirality : 0.039 0.205 1682 Planarity : 0.004 0.039 1804 Dihedral : 9.887 81.706 1556 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.80 % Allowed : 10.95 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.74 (0.23), residues: 1322 helix: 2.17 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 519 HIS 0.003 0.001 HIS B 600 PHE 0.015 0.001 PHE B 324 TYR 0.007 0.001 TYR A 542 ARG 0.003 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7328 (p) REVERT: B 269 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7391 (mmtt) REVERT: B 490 LEU cc_start: 0.7448 (tt) cc_final: 0.7128 (mt) REVERT: B 558 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7389 (p) outliers start: 20 outliers final: 12 residues processed: 175 average time/residue: 2.2759 time to fit residues: 435.1652 Evaluate side-chains 181 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10746 Z= 0.321 Angle : 0.532 7.081 14596 Z= 0.281 Chirality : 0.041 0.195 1682 Planarity : 0.005 0.041 1804 Dihedral : 10.234 85.257 1556 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.97 % Allowed : 11.31 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.46 (0.23), residues: 1322 helix: 1.94 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.76 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 519 HIS 0.003 0.001 HIS B 600 PHE 0.014 0.001 PHE B 324 TYR 0.009 0.001 TYR B 542 ARG 0.004 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 ARG cc_start: 0.7173 (ttm-80) cc_final: 0.6912 (ttm110) REVERT: B 269 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7416 (mmtt) REVERT: B 558 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7547 (p) outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 2.0134 time to fit residues: 388.2449 Evaluate side-chains 176 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10746 Z= 0.162 Angle : 0.479 7.142 14596 Z= 0.250 Chirality : 0.039 0.220 1682 Planarity : 0.004 0.038 1804 Dihedral : 9.717 81.578 1556 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 12.30 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.75 (0.23), residues: 1322 helix: 2.16 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 519 HIS 0.002 0.001 HIS B 600 PHE 0.014 0.001 PHE A 324 TYR 0.005 0.001 TYR A 542 ARG 0.005 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6896 (ttm110) REVERT: B 269 LYS cc_start: 0.7877 (mmmm) cc_final: 0.7366 (mmtt) outliers start: 18 outliers final: 12 residues processed: 177 average time/residue: 2.1051 time to fit residues: 410.3936 Evaluate side-chains 180 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10746 Z= 0.187 Angle : 0.480 7.075 14596 Z= 0.250 Chirality : 0.039 0.211 1682 Planarity : 0.004 0.038 1804 Dihedral : 9.446 80.598 1556 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.97 % Allowed : 12.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.81 (0.23), residues: 1322 helix: 2.20 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS A 600 PHE 0.015 0.001 PHE B 324 TYR 0.007 0.001 TYR B 392 ARG 0.004 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6897 (ttm110) REVERT: B 269 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7330 (mmtt) outliers start: 22 outliers final: 14 residues processed: 178 average time/residue: 2.0935 time to fit residues: 410.7317 Evaluate side-chains 180 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10746 Z= 0.216 Angle : 0.493 7.097 14596 Z= 0.258 Chirality : 0.039 0.213 1682 Planarity : 0.004 0.039 1804 Dihedral : 9.437 82.270 1556 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 13.02 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.73 (0.23), residues: 1322 helix: 2.15 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 519 HIS 0.003 0.001 HIS B 600 PHE 0.015 0.001 PHE B 324 TYR 0.011 0.001 TYR B 392 ARG 0.004 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7346 (mmtt) outliers start: 18 outliers final: 15 residues processed: 174 average time/residue: 2.0811 time to fit residues: 398.3126 Evaluate side-chains 180 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10746 Z= 0.225 Angle : 0.495 7.045 14596 Z= 0.259 Chirality : 0.040 0.216 1682 Planarity : 0.005 0.040 1804 Dihedral : 9.440 83.936 1556 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.44 % Allowed : 13.91 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.69 (0.23), residues: 1322 helix: 2.13 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS B 403 PHE 0.014 0.001 PHE A 324 TYR 0.009 0.001 TYR B 392 ARG 0.006 0.000 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7342 (mmtt) outliers start: 16 outliers final: 15 residues processed: 178 average time/residue: 2.0870 time to fit residues: 409.1852 Evaluate side-chains 181 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 785 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7893 > 50: distance: 209 - 217: 22.210 distance: 217 - 218: 20.447 distance: 217 - 222: 22.394 distance: 218 - 219: 33.478 distance: 218 - 221: 24.035 distance: 218 - 223: 30.754 distance: 219 - 220: 46.097 distance: 219 - 227: 14.866 distance: 221 - 224: 21.994 distance: 221 - 225: 22.598 distance: 221 - 226: 26.498 distance: 227 - 228: 36.198 distance: 227 - 239: 28.497 distance: 228 - 229: 26.089 distance: 228 - 231: 20.221 distance: 228 - 240: 30.558 distance: 229 - 230: 19.300 distance: 229 - 248: 15.755 distance: 231 - 232: 7.338 distance: 231 - 241: 8.310 distance: 231 - 242: 7.954 distance: 232 - 233: 10.104 distance: 232 - 234: 8.825 distance: 233 - 235: 7.841 distance: 233 - 243: 10.179 distance: 234 - 236: 7.804 distance: 234 - 244: 5.741 distance: 248 - 249: 14.166 distance: 248 - 254: 28.616 distance: 249 - 250: 31.436 distance: 249 - 252: 45.611 distance: 249 - 255: 26.731 distance: 250 - 251: 28.324 distance: 250 - 262: 30.247 distance: 252 - 253: 42.976 distance: 252 - 256: 26.652 distance: 252 - 257: 42.002 distance: 253 - 254: 29.721 distance: 253 - 258: 15.381 distance: 253 - 259: 11.798 distance: 254 - 260: 9.147 distance: 254 - 261: 18.791 distance: 262 - 263: 44.593 distance: 262 - 273: 38.093 distance: 263 - 264: 59.789 distance: 263 - 266: 33.849 distance: 263 - 274: 30.162 distance: 264 - 265: 26.987 distance: 264 - 286: 37.980 distance: 266 - 267: 12.461 distance: 266 - 275: 14.349 distance: 266 - 276: 10.584 distance: 267 - 268: 10.345 distance: 267 - 277: 9.055 distance: 267 - 278: 12.725 distance: 268 - 269: 10.513 distance: 268 - 279: 4.901 distance: 268 - 280: 3.413 distance: 269 - 270: 11.476 distance: 269 - 281: 9.996 distance: 270 - 271: 9.056 distance: 270 - 272: 4.758 distance: 271 - 282: 5.664 distance: 271 - 283: 5.918 distance: 272 - 284: 5.054 distance: 272 - 285: 3.743 distance: 286 - 287: 26.290 distance: 286 - 297: 17.345 distance: 287 - 288: 24.454 distance: 287 - 290: 30.456 distance: 287 - 298: 13.776 distance: 288 - 289: 31.082 distance: 288 - 306: 24.716 distance: 290 - 291: 38.729 distance: 290 - 299: 34.055 distance: 290 - 300: 32.646 distance: 291 - 292: 18.333 distance: 291 - 293: 11.712 distance: 292 - 294: 7.068 distance: 292 - 301: 5.840 distance: 293 - 295: 4.920 distance: 293 - 302: 5.945 distance: 294 - 296: 7.136 distance: 294 - 303: 5.196 distance: 295 - 296: 6.120 distance: 306 - 307: 35.988 distance: 306 - 312: 15.092 distance: 307 - 308: 18.527 distance: 307 - 310: 53.008 distance: 307 - 313: 19.519 distance: 308 - 309: 10.865 distance: 308 - 320: 37.125 distance: 310 - 311: 41.618 distance: 310 - 314: 35.009 distance: 310 - 315: 38.754 distance: 311 - 312: 16.155 distance: 311 - 316: 23.043 distance: 311 - 317: 17.091 distance: 312 - 318: 21.695 distance: 312 - 319: 33.087 distance: 320 - 321: 43.164 distance: 320 - 326: 29.791 distance: 321 - 322: 16.124 distance: 321 - 324: 16.944 distance: 321 - 327: 20.455 distance: 322 - 323: 36.120 distance: 322 - 334: 19.422 distance: 324 - 325: 16.429 distance: 324 - 328: 8.197 distance: 324 - 329: 10.567 distance: 325 - 326: 8.081 distance: 325 - 330: 3.805 distance: 325 - 331: 8.390 distance: 326 - 332: 8.015 distance: 326 - 333: 6.547 distance: 334 - 335: 20.206 distance: 334 - 342: 21.179 distance: 335 - 336: 28.596 distance: 335 - 338: 13.510 distance: 335 - 343: 23.072 distance: 336 - 337: 26.951 distance: 336 - 353: 30.216 distance: 338 - 339: 13.442 distance: 338 - 340: 10.587 distance: 338 - 344: 12.428 distance: 339 - 341: 12.265 distance: 339 - 345: 9.833 distance: 339 - 346: 10.590 distance: 340 - 347: 8.353 distance: 340 - 348: 4.952 distance: 340 - 349: 6.755 distance: 341 - 350: 3.166 distance: 341 - 351: 3.374 distance: 341 - 352: 5.163 distance: 353 - 354: 39.698 distance: 353 - 362: 4.935 distance: 354 - 355: 23.188 distance: 354 - 357: 17.416 distance: 354 - 363: 32.193 distance: 355 - 356: 7.005 distance: 355 - 370: 24.341 distance: 357 - 358: 11.004 distance: 357 - 364: 15.584 distance: 357 - 365: 7.240 distance: 358 - 359: 21.406 distance: 358 - 366: 13.388 distance: 358 - 367: 20.593 distance: 359 - 360: 15.303 distance: 359 - 361: 12.944 distance: 361 - 368: 11.567 distance: 361 - 369: 11.937 distance: 370 - 371: 19.394 distance: 370 - 376: 15.993 distance: 371 - 372: 12.461 distance: 371 - 374: 9.704 distance: 371 - 377: 15.818 distance: 372 - 373: 6.917 distance: 372 - 381: 4.758 distance: 374 - 375: 12.551 distance: 374 - 378: 10.926 distance: 374 - 379: 6.900 distance: 375 - 380: 6.954