Starting phenix.real_space_refine on Fri Feb 16 11:36:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/02_2024/7vnp_32044_neut_trim_updated.pdb" } resolution = 2.79 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= 0.030 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 56 5.16 5 C 9524 2.51 5 N 2516 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E ARG 535": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E ARG 575": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G ARG 535": "NH1" <-> "NH2" Residue "G ARG 538": "NH1" <-> "NH2" Residue "G ARG 547": "NH1" <-> "NH2" Residue "G ARG 575": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 7, 'TRANS': 324} Chain breaks: 2 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 7, 'TRANS': 324} Chain breaks: 2 Chain: "D" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 7, 'TRANS': 324} Chain breaks: 2 Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 7, 'TRANS': 324} Chain breaks: 2 Chain: "H" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 157 Unusual residues: {' K': 4, '7YV': 2, 'PT5': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PT5:plan-6': 2} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'7YV': 1, 'PT5': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PT5:plan-6': 2} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'7YV': 1, 'PT5': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PT5:plan-6': 2} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 115 Unusual residues: {'PT5': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PT5:plan-6': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 8.46, per 1000 atoms: 0.58 Number of scatterers: 14656 At special positions: 0 Unit cell: (127.1, 127.1, 112.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 56 16.00 P 24 15.00 O 2532 8.00 N 2516 7.00 C 9524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 96 through 120 Processing helix chain 'A' and resid 126 through 152 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 173 through 190 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 235 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.728A pdb=" N LEU A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 355 removed outlier: 3.749A pdb=" N LYS A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 529 through 551 removed outlier: 3.724A pdb=" N ARG A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.637A pdb=" N GLU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 67 through 72 removed outlier: 4.184A pdb=" N MET B 72 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.942A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 96 through 120 Processing helix chain 'C' and resid 126 through 152 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 173 through 190 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 235 through 260 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.729A pdb=" N LEU C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 355 removed outlier: 3.749A pdb=" N LYS C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 338 " --> pdb=" O HIS C 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 529 through 551 removed outlier: 3.724A pdb=" N ARG C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 583 Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.637A pdb=" N GLU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.184A pdb=" N MET D 72 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 removed outlier: 3.942A pdb=" N PHE D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'E' and resid 75 through 92 Processing helix chain 'E' and resid 96 through 120 Processing helix chain 'E' and resid 126 through 152 Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 173 through 190 Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 223 through 233 Processing helix chain 'E' and resid 235 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 311 removed outlier: 3.728A pdb=" N LEU E 306 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 355 removed outlier: 3.748A pdb=" N LYS E 337 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E 338 " --> pdb=" O HIS E 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 529 through 551 removed outlier: 3.724A pdb=" N ARG E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 583 Processing helix chain 'F' and resid 7 through 19 removed outlier: 3.637A pdb=" N GLU F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 55 Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.183A pdb=" N MET F 72 " --> pdb=" O PHE F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 93 removed outlier: 3.943A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 96 through 120 Processing helix chain 'G' and resid 126 through 152 Processing helix chain 'G' and resid 162 through 171 Processing helix chain 'G' and resid 173 through 190 Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'G' and resid 223 through 233 Processing helix chain 'G' and resid 235 through 260 Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 311 removed outlier: 3.728A pdb=" N LEU G 306 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 355 removed outlier: 3.748A pdb=" N LYS G 337 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG G 338 " --> pdb=" O HIS G 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) Proline residue: G 341 - end of helix Processing helix chain 'G' and resid 529 through 551 removed outlier: 3.724A pdb=" N ARG G 547 " --> pdb=" O LEU G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 583 Processing helix chain 'H' and resid 7 through 19 removed outlier: 3.638A pdb=" N GLU H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 67 through 72 removed outlier: 4.183A pdb=" N MET H 72 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.943A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 128 Processing helix chain 'H' and resid 139 through 147 1032 hydrogen bonds defined for protein. 2808 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: 4.36 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2189 1.30 - 1.43: 4235 1.43 - 1.56: 8420 1.56 - 1.69: 40 1.69 - 1.82: 88 Bond restraints: 14972 Sorted by residual: bond pdb=" C04 7YV C1103 " pdb=" C05 7YV C1103 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV A1108 " pdb=" C05 7YV A1108 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C04 7YV E1103 " pdb=" C05 7YV E1103 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C04 7YV A1107 " pdb=" C05 7YV A1107 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C03 7YV A1107 " pdb=" C05 7YV A1107 " ideal model delta sigma weight residual 1.531 1.304 0.227 2.00e-02 2.50e+03 1.28e+02 ... (remaining 14967 not shown) Histogram of bond angle deviations from ideal: 92.63 - 101.42: 48 101.42 - 110.22: 3409 110.22 - 119.01: 8691 119.01 - 127.80: 8020 127.80 - 136.60: 140 Bond angle restraints: 20308 Sorted by residual: angle pdb=" C18 PT5 C1101 " pdb=" C19 PT5 C1101 " pdb=" C20 PT5 C1101 " ideal model delta sigma weight residual 85.86 125.78 -39.92 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C18 PT5 G1101 " pdb=" C19 PT5 G1101 " pdb=" C20 PT5 G1101 " ideal model delta sigma weight residual 85.86 125.75 -39.89 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C18 PT5 A1101 " pdb=" C19 PT5 A1101 " pdb=" C20 PT5 A1101 " ideal model delta sigma weight residual 85.86 125.73 -39.87 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C18 PT5 E1101 " pdb=" C19 PT5 E1101 " pdb=" C20 PT5 E1101 " ideal model delta sigma weight residual 85.86 125.71 -39.85 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 C1102 " pdb=" C19 PT5 C1102 " pdb=" C20 PT5 C1102 " ideal model delta sigma weight residual 85.86 125.62 -39.76 3.00e+00 1.11e-01 1.76e+02 ... (remaining 20303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 8124 27.51 - 55.03: 463 55.03 - 82.54: 73 82.54 - 110.06: 28 110.06 - 137.57: 20 Dihedral angle restraints: 8708 sinusoidal: 3200 harmonic: 5508 Sorted by residual: dihedral pdb=" CA LEU E 553 " pdb=" C LEU E 553 " pdb=" N ARG E 554 " pdb=" CA ARG E 554 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU G 553 " pdb=" C LEU G 553 " pdb=" N ARG G 554 " pdb=" CA ARG G 554 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU A 553 " pdb=" C LEU A 553 " pdb=" N ARG A 554 " pdb=" CA ARG A 554 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 8705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2231 0.151 - 0.302: 73 0.302 - 0.453: 0 0.453 - 0.604: 0 0.604 - 0.755: 8 Chirality restraints: 2312 Sorted by residual: chirality pdb=" C03 7YV E1103 " pdb=" C05 7YV E1103 " pdb=" C06 7YV E1103 " pdb=" C08 7YV E1103 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C03 7YV A1107 " pdb=" C05 7YV A1107 " pdb=" C06 7YV A1107 " pdb=" C08 7YV A1107 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C03 7YV C1103 " pdb=" C05 7YV C1103 " pdb=" C06 7YV C1103 " pdb=" C08 7YV C1103 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 2309 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 PT5 G1101 " -0.241 2.00e-02 2.50e+03 2.41e-01 5.82e+02 pdb=" C15 PT5 G1101 " 0.242 2.00e-02 2.50e+03 pdb=" C16 PT5 G1101 " 0.241 2.00e-02 2.50e+03 pdb=" C17 PT5 G1101 " -0.241 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 E1101 " -0.241 2.00e-02 2.50e+03 2.41e-01 5.82e+02 pdb=" C15 PT5 E1101 " 0.241 2.00e-02 2.50e+03 pdb=" C16 PT5 E1101 " 0.242 2.00e-02 2.50e+03 pdb=" C17 PT5 E1101 " -0.241 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 A1101 " 0.241 2.00e-02 2.50e+03 2.41e-01 5.80e+02 pdb=" C15 PT5 A1101 " -0.241 2.00e-02 2.50e+03 pdb=" C16 PT5 A1101 " -0.241 2.00e-02 2.50e+03 pdb=" C17 PT5 A1101 " 0.241 2.00e-02 2.50e+03 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 308 2.67 - 3.29: 18242 3.29 - 3.90: 29269 3.90 - 4.52: 39081 4.52 - 5.14: 55908 Nonbonded interactions: 142808 Sorted by model distance: nonbonded pdb=" O41 PT5 E1101 " pdb=" O6 PT5 E1101 " model vdw 2.052 2.440 nonbonded pdb=" O41 PT5 G1101 " pdb=" O6 PT5 G1101 " model vdw 2.052 2.440 nonbonded pdb=" O41 PT5 A1101 " pdb=" O6 PT5 A1101 " model vdw 2.052 2.440 nonbonded pdb=" O41 PT5 C1101 " pdb=" O6 PT5 C1101 " model vdw 2.052 2.440 nonbonded pdb=" O2 PT5 C1101 " pdb=" O5 PT5 C1101 " model vdw 2.072 2.440 ... (remaining 142803 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 74 through 584 or resid 1101 through 1102)) selection = (chain 'C' and (resid 74 through 584 or resid 1101 through 1102)) selection = (chain 'E' and (resid 74 through 584 or resid 1101 through 1102)) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.550 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.350 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 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:15.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 : 0.014 0.235 14972 Z= 0.958 Angle : 1.690 39.920 20308 Z= 0.769 Chirality : 0.071 0.755 2312 Planarity : 0.017 0.241 2504 Dihedral : 19.757 137.570 5148 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.98 % Favored : 93.59 % Rotamer: Outliers : 7.99 % Allowed : 4.79 % Favored : 87.22 % 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: -0.27 (0.19), residues: 1872 helix: 0.58 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 275 HIS 0.007 0.001 HIS E 102 PHE 0.040 0.002 PHE G 311 TYR 0.016 0.002 TYR F 139 ARG 0.006 0.001 ARG G 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 281 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6657 (mmm160) REVERT: A 126 GLU cc_start: 0.7626 (pm20) cc_final: 0.7354 (pm20) REVERT: A 261 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7648 (ttmm) REVERT: A 320 SER cc_start: 0.7842 (t) cc_final: 0.7413 (m) REVERT: A 541 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6676 (mmpt) REVERT: A 552 THR cc_start: 0.7464 (p) cc_final: 0.7054 (p) REVERT: A 565 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6428 (t80) REVERT: A 575 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7815 (ptp-110) REVERT: B 115 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5688 (mp0) REVERT: C 126 GLU cc_start: 0.7620 (pm20) cc_final: 0.7333 (pm20) REVERT: C 261 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7677 (ttmm) REVERT: C 320 SER cc_start: 0.7885 (t) cc_final: 0.7431 (m) REVERT: C 328 GLU cc_start: 0.7521 (tp30) cc_final: 0.7260 (tp30) REVERT: C 541 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6809 (mmpt) REVERT: C 552 THR cc_start: 0.7495 (p) cc_final: 0.7250 (p) REVERT: D 108 HIS cc_start: 0.8278 (t-90) cc_final: 0.8051 (t-90) REVERT: D 115 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5696 (mp0) REVERT: E 95 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6649 (mmm160) REVERT: E 126 GLU cc_start: 0.7554 (pm20) cc_final: 0.7223 (pm20) REVERT: E 261 LYS cc_start: 0.7901 (ttpp) cc_final: 0.7593 (ttmm) REVERT: E 320 SER cc_start: 0.7884 (t) cc_final: 0.7446 (m) REVERT: E 328 GLU cc_start: 0.7585 (tp30) cc_final: 0.7353 (tp30) REVERT: E 541 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6768 (mmpt) REVERT: F 115 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5632 (mp0) REVERT: G 95 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6763 (mmm160) REVERT: G 126 GLU cc_start: 0.7530 (pm20) cc_final: 0.7322 (pm20) REVERT: G 320 SER cc_start: 0.7877 (t) cc_final: 0.7512 (m) REVERT: G 541 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6810 (mmpt) REVERT: G 552 THR cc_start: 0.7534 (p) cc_final: 0.7231 (p) REVERT: G 575 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7771 (ptp-170) REVERT: H 108 HIS cc_start: 0.8259 (t-90) cc_final: 0.8016 (t-90) REVERT: H 115 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5831 (mp0) outliers start: 100 outliers final: 16 residues processed: 356 average time/residue: 1.3284 time to fit residues: 515.6247 Evaluate side-chains 241 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 219 ARG Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 579 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 108 HIS B 112 ASN F 108 HIS F 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14972 Z= 0.208 Angle : 0.632 9.302 20308 Z= 0.317 Chirality : 0.037 0.143 2312 Planarity : 0.004 0.026 2504 Dihedral : 15.086 93.796 2488 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.73 % Rotamer: Outliers : 4.07 % Allowed : 20.61 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1872 helix: 1.50 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -2.32 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 275 HIS 0.008 0.001 HIS C 569 PHE 0.015 0.002 PHE E 174 TYR 0.020 0.001 TYR E 80 ARG 0.009 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.657 Fit side-chains REVERT: A 210 GLN cc_start: 0.6459 (mp10) cc_final: 0.6110 (mp10) REVERT: A 320 SER cc_start: 0.7879 (t) cc_final: 0.7595 (m) REVERT: A 547 ARG cc_start: 0.8760 (ttt90) cc_final: 0.8280 (tpp80) REVERT: A 575 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7802 (ttm110) REVERT: B 115 GLU cc_start: 0.6323 (mm-30) cc_final: 0.5950 (mp0) REVERT: C 148 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7119 (mp) REVERT: C 210 GLN cc_start: 0.6440 (mp10) cc_final: 0.6110 (mp10) REVERT: C 320 SER cc_start: 0.7868 (t) cc_final: 0.7588 (m) REVERT: C 328 GLU cc_start: 0.7492 (tp30) cc_final: 0.7247 (tp30) REVERT: C 340 MET cc_start: 0.8361 (tpt) cc_final: 0.8147 (mmp) REVERT: C 547 ARG cc_start: 0.8623 (ttt90) cc_final: 0.8243 (tpp80) REVERT: D 115 GLU cc_start: 0.6232 (mm-30) cc_final: 0.5824 (mp0) REVERT: E 210 GLN cc_start: 0.6405 (mp10) cc_final: 0.6105 (mp10) REVERT: E 212 LEU cc_start: 0.6997 (tt) cc_final: 0.6692 (pp) REVERT: E 320 SER cc_start: 0.7848 (t) cc_final: 0.7598 (m) REVERT: E 547 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8114 (mmm-85) REVERT: E 551 GLU cc_start: 0.8145 (pm20) cc_final: 0.7649 (pm20) REVERT: F 115 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5953 (mp0) REVERT: G 210 GLN cc_start: 0.6401 (mp10) cc_final: 0.6143 (mp10) REVERT: G 320 SER cc_start: 0.7885 (t) cc_final: 0.7620 (m) REVERT: G 340 MET cc_start: 0.8461 (mmp) cc_final: 0.8246 (mmp) REVERT: G 547 ARG cc_start: 0.8816 (ttt90) cc_final: 0.8364 (tpp80) REVERT: G 565 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5732 (t80) REVERT: H 115 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5840 (mp0) outliers start: 51 outliers final: 8 residues processed: 273 average time/residue: 1.0428 time to fit residues: 317.5895 Evaluate side-chains 227 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 557 ASP Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain G residue 579 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 108 HIS B 112 ASN C 85 ASN D 108 HIS D 112 ASN E 85 ASN F 108 HIS F 112 ASN G 85 ASN H 108 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.101 14972 Z= 0.697 Angle : 0.832 12.236 20308 Z= 0.412 Chirality : 0.047 0.215 2312 Planarity : 0.006 0.045 2504 Dihedral : 16.269 127.547 2424 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 6.23 % Allowed : 21.96 % Favored : 71.81 % 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: -0.25 (0.18), residues: 1872 helix: 0.57 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.68 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 275 HIS 0.008 0.002 HIS A 102 PHE 0.027 0.003 PHE G 310 TYR 0.015 0.003 TYR E 80 ARG 0.007 0.001 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 227 time to evaluate : 1.551 Fit side-chains REVERT: A 139 MET cc_start: 0.7652 (mtp) cc_final: 0.7449 (mtp) REVERT: A 171 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7015 (ttm110) REVERT: A 336 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 547 ARG cc_start: 0.8841 (ttt90) cc_final: 0.8375 (tpp80) REVERT: B 115 GLU cc_start: 0.6357 (mm-30) cc_final: 0.5979 (mp0) REVERT: C 171 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6328 (ttm110) REVERT: C 336 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 547 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8261 (mtm110) REVERT: D 115 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5926 (mp0) REVERT: E 130 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7691 (mt-10) REVERT: E 139 MET cc_start: 0.7646 (mtp) cc_final: 0.7377 (mtp) REVERT: E 212 LEU cc_start: 0.7618 (tt) cc_final: 0.7099 (pp) REVERT: E 344 ASN cc_start: 0.7966 (m-40) cc_final: 0.7689 (m-40) REVERT: E 547 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8321 (mtt90) REVERT: F 115 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5994 (mp0) REVERT: G 214 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7228 (ttp) REVERT: H 115 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5987 (mp0) outliers start: 78 outliers final: 23 residues processed: 276 average time/residue: 0.9126 time to fit residues: 284.8644 Evaluate side-chains 238 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain G residue 579 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 40.0000 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 50.0000 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 108 HIS C 85 ASN C 125 GLN D 108 HIS E 85 ASN G 85 ASN G 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14972 Z= 0.213 Angle : 0.595 9.261 20308 Z= 0.298 Chirality : 0.037 0.374 2312 Planarity : 0.004 0.032 2504 Dihedral : 13.825 86.730 2420 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.05 % Rotamer: Outliers : 5.11 % Allowed : 24.76 % Favored : 70.13 % 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: 0.86 (0.19), residues: 1872 helix: 1.38 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -2.26 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 152 HIS 0.010 0.001 HIS B 108 PHE 0.016 0.001 PHE E 167 TYR 0.023 0.001 TYR C 80 ARG 0.009 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8127 (t) cc_final: 0.7755 (m) REVERT: A 171 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6939 (ttm110) REVERT: A 320 SER cc_start: 0.7877 (t) cc_final: 0.7557 (m) REVERT: A 336 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 339 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8375 (tpp80) REVERT: A 547 ARG cc_start: 0.8819 (ttt90) cc_final: 0.8370 (tpp80) REVERT: B 115 GLU cc_start: 0.6254 (mm-30) cc_final: 0.5932 (mp0) REVERT: C 119 SER cc_start: 0.8125 (t) cc_final: 0.7740 (m) REVERT: C 320 SER cc_start: 0.7881 (t) cc_final: 0.7566 (m) REVERT: C 336 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: C 547 ARG cc_start: 0.8754 (ttt90) cc_final: 0.8207 (mtm110) REVERT: D 115 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5962 (mp0) REVERT: E 119 SER cc_start: 0.8101 (t) cc_final: 0.7707 (m) REVERT: E 171 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6884 (ttm110) REVERT: E 320 SER cc_start: 0.7891 (t) cc_final: 0.7539 (m) REVERT: E 333 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6502 (ttmm) REVERT: E 336 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: E 344 ASN cc_start: 0.7996 (m-40) cc_final: 0.7641 (m-40) REVERT: E 547 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8009 (mmm-85) REVERT: E 551 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: F 66 PHE cc_start: 0.4142 (OUTLIER) cc_final: 0.3904 (p90) REVERT: F 115 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5960 (mp0) REVERT: G 320 SER cc_start: 0.7879 (t) cc_final: 0.7554 (m) REVERT: G 336 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: G 547 ARG cc_start: 0.8823 (ttt90) cc_final: 0.8234 (mtm110) REVERT: G 554 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6713 (ptt-90) REVERT: H 115 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5986 (mp0) outliers start: 64 outliers final: 18 residues processed: 269 average time/residue: 0.9562 time to fit residues: 290.0683 Evaluate side-chains 235 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain G residue 579 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 92 optimal weight: 50.0000 chunk 163 optimal weight: 0.1980 chunk 45 optimal weight: 50.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 125 GLN A 580 GLN B 108 HIS C 85 ASN C 125 GLN C 580 GLN D 108 HIS D 112 ASN E 85 ASN F 108 HIS G 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14972 Z= 0.258 Angle : 0.600 10.510 20308 Z= 0.299 Chirality : 0.038 0.377 2312 Planarity : 0.004 0.030 2504 Dihedral : 13.410 87.754 2420 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.05 % Rotamer: Outliers : 4.79 % Allowed : 25.00 % Favored : 70.21 % 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: 1.06 (0.20), residues: 1872 helix: 1.53 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.015 0.002 HIS C 569 PHE 0.017 0.002 PHE E 167 TYR 0.015 0.001 TYR C 565 ARG 0.010 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 1.624 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: A 119 SER cc_start: 0.8124 (t) cc_final: 0.7782 (m) REVERT: A 171 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6952 (ttm110) REVERT: A 320 SER cc_start: 0.7877 (t) cc_final: 0.7562 (m) REVERT: A 547 ARG cc_start: 0.8821 (ttt90) cc_final: 0.8399 (tpp80) REVERT: B 115 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5947 (mp0) REVERT: C 320 SER cc_start: 0.7880 (t) cc_final: 0.7565 (m) REVERT: C 336 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: D 113 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.6887 (pp) REVERT: D 115 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5831 (mp0) REVERT: E 119 SER cc_start: 0.8155 (t) cc_final: 0.7794 (m) REVERT: E 171 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6779 (ttm110) REVERT: E 320 SER cc_start: 0.7872 (t) cc_final: 0.7552 (m) REVERT: E 333 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6547 (ttmm) REVERT: E 336 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: E 344 ASN cc_start: 0.8027 (m-40) cc_final: 0.7686 (m-40) REVERT: E 547 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8002 (mmm-85) REVERT: E 551 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: F 115 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6063 (mp0) REVERT: G 119 SER cc_start: 0.8253 (t) cc_final: 0.7783 (m) REVERT: G 320 SER cc_start: 0.7872 (t) cc_final: 0.7559 (m) REVERT: G 547 ARG cc_start: 0.8845 (ttt90) cc_final: 0.8374 (tpp80) REVERT: G 550 LYS cc_start: 0.8034 (tppt) cc_final: 0.7726 (tppt) REVERT: G 554 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6783 (ptt-90) REVERT: H 115 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6055 (mp0) outliers start: 60 outliers final: 27 residues processed: 251 average time/residue: 1.0062 time to fit residues: 283.4233 Evaluate side-chains 246 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 50.0000 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN B 108 HIS B 112 ASN C 125 GLN C 580 GLN E 85 ASN F 108 HIS F 112 ASN G 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14972 Z= 0.227 Angle : 0.588 9.479 20308 Z= 0.292 Chirality : 0.037 0.353 2312 Planarity : 0.004 0.031 2504 Dihedral : 12.872 85.269 2420 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.15 % Rotamer: Outliers : 4.79 % Allowed : 25.72 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1872 helix: 1.68 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 350 HIS 0.014 0.001 HIS C 569 PHE 0.018 0.001 PHE E 167 TYR 0.017 0.001 TYR C 565 ARG 0.010 0.000 ARG C 538 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6954 (ttm110) REVERT: A 320 SER cc_start: 0.7867 (t) cc_final: 0.7598 (m) REVERT: A 336 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 547 ARG cc_start: 0.8786 (ttt90) cc_final: 0.8354 (tpp80) REVERT: B 109 VAL cc_start: 0.8152 (p) cc_final: 0.7938 (p) REVERT: B 113 LEU cc_start: 0.7484 (tp) cc_final: 0.6822 (pp) REVERT: B 115 GLU cc_start: 0.6351 (mm-30) cc_final: 0.6021 (mp0) REVERT: C 320 SER cc_start: 0.7869 (t) cc_final: 0.7602 (m) REVERT: C 336 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: C 543 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5896 (tm) REVERT: D 109 VAL cc_start: 0.8192 (p) cc_final: 0.7977 (p) REVERT: D 113 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6925 (pp) REVERT: D 115 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5772 (mp0) REVERT: E 77 HIS cc_start: 0.6304 (t-90) cc_final: 0.6012 (t70) REVERT: E 171 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6790 (ttm110) REVERT: E 320 SER cc_start: 0.7873 (t) cc_final: 0.7594 (m) REVERT: E 333 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6486 (ttmm) REVERT: E 336 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: E 344 ASN cc_start: 0.8018 (m-40) cc_final: 0.7565 (m-40) REVERT: E 547 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8114 (tpp80) REVERT: F 115 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5994 (mp0) REVERT: G 119 SER cc_start: 0.8210 (t) cc_final: 0.7748 (m) REVERT: G 320 SER cc_start: 0.7866 (t) cc_final: 0.7598 (m) REVERT: G 336 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: G 547 ARG cc_start: 0.8828 (ttt90) cc_final: 0.8212 (mtm110) REVERT: G 550 LYS cc_start: 0.8043 (tppt) cc_final: 0.7791 (tppt) REVERT: G 554 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6732 (ptt-90) REVERT: H 115 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6127 (mp0) outliers start: 60 outliers final: 26 residues processed: 246 average time/residue: 0.9494 time to fit residues: 263.4081 Evaluate side-chains 239 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain G residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 102 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 181 optimal weight: 50.0000 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN C 125 GLN C 580 GLN D 108 HIS E 84 GLN E 85 ASN F 108 HIS F 112 ASN G 125 GLN ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14972 Z= 0.182 Angle : 0.569 9.349 20308 Z= 0.282 Chirality : 0.036 0.315 2312 Planarity : 0.004 0.032 2504 Dihedral : 12.320 84.579 2414 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Rotamer: Outliers : 4.55 % Allowed : 27.08 % Favored : 68.37 % 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 (0.19), residues: 1872 helix: 1.81 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -2.42 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 350 HIS 0.014 0.001 HIS C 569 PHE 0.018 0.001 PHE E 167 TYR 0.014 0.001 TYR A 80 ARG 0.005 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ILE cc_start: 0.7500 (mm) cc_final: 0.7192 (mt) REVERT: A 171 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6937 (ttm110) REVERT: A 320 SER cc_start: 0.7888 (t) cc_final: 0.7633 (m) REVERT: A 324 LEU cc_start: 0.8408 (tp) cc_final: 0.8116 (tt) REVERT: A 328 GLU cc_start: 0.7454 (tp30) cc_final: 0.7040 (mt-10) REVERT: A 547 ARG cc_start: 0.8796 (ttt90) cc_final: 0.8363 (tpp80) REVERT: B 115 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5856 (mp0) REVERT: C 214 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6392 (tpp) REVERT: C 320 SER cc_start: 0.7891 (t) cc_final: 0.7637 (m) REVERT: C 336 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: C 543 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.4664 (tm) REVERT: C 547 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8464 (ptp-170) REVERT: D 113 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6878 (pp) REVERT: D 115 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5808 (mp0) REVERT: E 77 HIS cc_start: 0.6317 (t-90) cc_final: 0.6035 (t70) REVERT: E 171 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6851 (ttm110) REVERT: E 320 SER cc_start: 0.7866 (t) cc_final: 0.7636 (m) REVERT: E 336 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: E 344 ASN cc_start: 0.8045 (m-40) cc_final: 0.7531 (m-40) REVERT: E 547 ARG cc_start: 0.8598 (ttt90) cc_final: 0.8071 (mtm110) REVERT: F 115 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5970 (mp0) REVERT: G 320 SER cc_start: 0.7887 (t) cc_final: 0.7633 (m) REVERT: G 324 LEU cc_start: 0.8406 (tp) cc_final: 0.8114 (tt) REVERT: G 328 GLU cc_start: 0.7456 (tp30) cc_final: 0.7041 (mt-10) REVERT: G 550 LYS cc_start: 0.8041 (tppt) cc_final: 0.7810 (tppt) REVERT: G 554 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6675 (ptt-90) REVERT: H 115 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6111 (mp0) outliers start: 57 outliers final: 22 residues processed: 256 average time/residue: 0.9280 time to fit residues: 269.6065 Evaluate side-chains 240 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 0.0000 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN B 112 ASN C 125 GLN C 580 GLN F 108 HIS F 112 ASN G 125 GLN G 580 GLN ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14972 Z= 0.299 Angle : 0.630 10.612 20308 Z= 0.311 Chirality : 0.039 0.464 2312 Planarity : 0.004 0.034 2504 Dihedral : 12.705 87.548 2412 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.73 % Rotamer: Outliers : 3.75 % Allowed : 28.59 % Favored : 67.65 % 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: 1.20 (0.19), residues: 1872 helix: 1.65 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 350 HIS 0.015 0.002 HIS C 569 PHE 0.021 0.002 PHE A 246 TYR 0.024 0.001 TYR C 565 ARG 0.004 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 212 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6917 (ttm110) REVERT: A 320 SER cc_start: 0.7872 (t) cc_final: 0.7537 (m) REVERT: B 115 GLU cc_start: 0.6258 (mm-30) cc_final: 0.5908 (mp0) REVERT: C 320 SER cc_start: 0.7881 (t) cc_final: 0.7551 (m) REVERT: C 336 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 543 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.4457 (tm) REVERT: C 547 ARG cc_start: 0.8771 (mtp180) cc_final: 0.8477 (ptp-170) REVERT: D 113 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7261 (tm) REVERT: D 115 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5777 (mp0) REVERT: E 77 HIS cc_start: 0.6327 (t-90) cc_final: 0.6015 (t70) REVERT: E 171 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6850 (ttm110) REVERT: E 320 SER cc_start: 0.7890 (t) cc_final: 0.7553 (m) REVERT: E 333 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6541 (ttmm) REVERT: E 336 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: E 344 ASN cc_start: 0.8014 (m-40) cc_final: 0.7574 (m-40) REVERT: E 547 ARG cc_start: 0.8667 (ttt90) cc_final: 0.8131 (mtm110) REVERT: F 115 GLU cc_start: 0.6361 (mm-30) cc_final: 0.6048 (mp0) REVERT: G 134 ILE cc_start: 0.7560 (mm) cc_final: 0.7355 (mt) REVERT: G 210 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5647 (mp10) REVERT: G 320 SER cc_start: 0.7873 (t) cc_final: 0.7537 (m) REVERT: G 547 ARG cc_start: 0.8825 (ttt90) cc_final: 0.8211 (mtm110) REVERT: G 554 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6689 (ptt-90) REVERT: H 115 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6174 (mp0) outliers start: 47 outliers final: 24 residues processed: 236 average time/residue: 1.0193 time to fit residues: 269.6223 Evaluate side-chains 239 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 50.0000 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN B 112 ASN C 85 ASN C 125 GLN C 580 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 125 GLN F 108 HIS F 112 ASN G 125 GLN G 580 GLN H 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14972 Z= 0.218 Angle : 0.596 10.863 20308 Z= 0.296 Chirality : 0.037 0.409 2312 Planarity : 0.004 0.033 2504 Dihedral : 12.479 85.735 2412 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 28.67 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1872 helix: 1.78 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.38 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 350 HIS 0.015 0.001 HIS C 569 PHE 0.021 0.001 PHE G 246 TYR 0.023 0.001 TYR C 565 ARG 0.004 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 1.530 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: A 134 ILE cc_start: 0.7660 (mm) cc_final: 0.7455 (mt) REVERT: A 171 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6906 (ttm110) REVERT: A 320 SER cc_start: 0.7892 (t) cc_final: 0.7619 (m) REVERT: A 324 LEU cc_start: 0.8362 (tp) cc_final: 0.8082 (tt) REVERT: A 327 GLN cc_start: 0.6948 (tp-100) cc_final: 0.6434 (mp10) REVERT: A 328 GLU cc_start: 0.7441 (tp30) cc_final: 0.7029 (mt-10) REVERT: A 336 GLU cc_start: 0.7813 (mp0) cc_final: 0.7596 (mp0) REVERT: B 115 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5895 (mp0) REVERT: C 320 SER cc_start: 0.7868 (t) cc_final: 0.7594 (m) REVERT: C 324 LEU cc_start: 0.8402 (tp) cc_final: 0.8139 (tt) REVERT: C 328 GLU cc_start: 0.7470 (tp30) cc_final: 0.7078 (mt-10) REVERT: C 336 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: C 543 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5693 (tm) REVERT: D 115 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6016 (mp0) REVERT: E 77 HIS cc_start: 0.6314 (t-90) cc_final: 0.6039 (t70) REVERT: E 320 SER cc_start: 0.7868 (t) cc_final: 0.7589 (m) REVERT: E 336 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: E 344 ASN cc_start: 0.8059 (m-40) cc_final: 0.7587 (m-40) REVERT: E 547 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7962 (mtm110) REVERT: E 551 GLU cc_start: 0.8143 (pm20) cc_final: 0.7683 (pm20) REVERT: F 115 GLU cc_start: 0.6348 (mm-30) cc_final: 0.6068 (mp0) REVERT: G 134 ILE cc_start: 0.7512 (mm) cc_final: 0.7300 (mt) REVERT: G 320 SER cc_start: 0.7847 (t) cc_final: 0.7591 (m) REVERT: G 324 LEU cc_start: 0.8369 (tp) cc_final: 0.8069 (tt) REVERT: G 328 GLU cc_start: 0.7441 (tp30) cc_final: 0.7071 (mt-10) REVERT: G 547 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8206 (mtm110) REVERT: G 554 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6673 (ptt-90) REVERT: H 73 MET cc_start: 0.6198 (tpt) cc_final: 0.5758 (tpp) REVERT: H 115 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6204 (mp0) outliers start: 42 outliers final: 25 residues processed: 236 average time/residue: 0.9875 time to fit residues: 262.6034 Evaluate side-chains 243 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 547 ARG Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN C 125 GLN C 580 GLN D 108 HIS F 112 ASN G 85 ASN G 125 GLN H 108 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14972 Z= 0.200 Angle : 0.600 10.421 20308 Z= 0.295 Chirality : 0.037 0.397 2312 Planarity : 0.004 0.032 2504 Dihedral : 12.329 85.414 2412 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.58 % Favored : 96.21 % Rotamer: Outliers : 2.64 % Allowed : 29.63 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1872 helix: 1.85 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.38 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 350 HIS 0.013 0.001 HIS C 569 PHE 0.021 0.001 PHE A 246 TYR 0.022 0.001 TYR C 565 ARG 0.009 0.000 ARG E 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.573 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: A 134 ILE cc_start: 0.7532 (mm) cc_final: 0.7329 (mt) REVERT: A 171 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6902 (ttm110) REVERT: A 320 SER cc_start: 0.7895 (t) cc_final: 0.7636 (m) REVERT: A 328 GLU cc_start: 0.7447 (tp30) cc_final: 0.7079 (mt-10) REVERT: B 73 MET cc_start: 0.6271 (tpt) cc_final: 0.5796 (tpp) REVERT: B 115 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5949 (mp0) REVERT: C 320 SER cc_start: 0.7893 (t) cc_final: 0.7627 (m) REVERT: C 328 GLU cc_start: 0.7465 (tp30) cc_final: 0.7082 (mt-10) REVERT: C 336 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 543 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5689 (tm) REVERT: D 115 GLU cc_start: 0.6243 (mm-30) cc_final: 0.5861 (mp0) REVERT: E 77 HIS cc_start: 0.6249 (t-90) cc_final: 0.5954 (t70) REVERT: E 320 SER cc_start: 0.7898 (t) cc_final: 0.7636 (m) REVERT: E 336 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: E 344 ASN cc_start: 0.8088 (m-40) cc_final: 0.7597 (m-40) REVERT: E 547 ARG cc_start: 0.8625 (ttt90) cc_final: 0.8153 (mtm110) REVERT: F 115 GLU cc_start: 0.6351 (mm-30) cc_final: 0.6088 (mp0) REVERT: G 134 ILE cc_start: 0.7576 (mm) cc_final: 0.7375 (mt) REVERT: G 210 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5461 (mp10) REVERT: G 320 SER cc_start: 0.7889 (t) cc_final: 0.7635 (m) REVERT: G 328 GLU cc_start: 0.7467 (tp30) cc_final: 0.7073 (mt-10) REVERT: G 547 ARG cc_start: 0.8806 (ttt90) cc_final: 0.8201 (mtm110) REVERT: H 73 MET cc_start: 0.6201 (tpt) cc_final: 0.5733 (tpp) REVERT: H 115 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6214 (mp0) outliers start: 33 outliers final: 22 residues processed: 235 average time/residue: 0.9998 time to fit residues: 266.8191 Evaluate side-chains 243 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 565 TYR Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 565 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 50.0000 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 125 GLN A 580 GLN B 112 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 580 GLN D 108 HIS D 112 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 125 GLN H 108 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.250568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137056 restraints weight = 15131.592| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.84 r_work: 0.3208 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14972 Z= 0.378 Angle : 0.672 10.652 20308 Z= 0.331 Chirality : 0.041 0.430 2312 Planarity : 0.004 0.036 2504 Dihedral : 12.939 93.122 2412 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.95 % Favored : 95.83 % Rotamer: Outliers : 2.96 % Allowed : 29.63 % Favored : 67.41 % 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: 1.11 (0.19), residues: 1872 helix: 1.60 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 350 HIS 0.012 0.002 HIS C 569 PHE 0.024 0.002 PHE A 246 TYR 0.025 0.002 TYR C 565 ARG 0.008 0.000 ARG C 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5558.57 seconds wall clock time: 99 minutes 15.42 seconds (5955.42 seconds total)