Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 14:57:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_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_32044/04_2023/7vnp_32044_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnp_32044/04_2023/7vnp_32044_neut_trim_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 7.33, per 1000 atoms: 0.50 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: 6.44 Conformation dependent library (CDL) restraints added in 2.3 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: 1.16 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: 4.06 Time building geometry restraints manager: 6.95 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: 8004 27.51 - 55.03: 451 55.03 - 82.54: 65 82.54 - 110.06: 24 110.06 - 137.57: 20 Dihedral angle restraints: 8564 sinusoidal: 3056 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 8561 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: 1.180 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: 7.100 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 39.230 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.890 ------------------------------------------------------------------------------- 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 : 19.417 137.570 5004 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 % 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 *********************** 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 : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 16 residues processed: 356 average time/residue: 1.3425 time to fit residues: 520.3738 Evaluate side-chains 219 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 2.1089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 6.9990 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 D 112 ASN F 108 HIS F 112 ASN H 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14972 Z= 0.213 Angle : 0.645 9.936 20308 Z= 0.325 Chirality : 0.038 0.148 2312 Planarity : 0.005 0.034 2504 Dihedral : 13.398 93.263 2268 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.05 % Rotamer Outliers : 4.39 % 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: 0.95 (0.20), residues: 1872 helix: 1.44 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.27 (0.31), residues: 420 *********************** 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 299 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 1.675 Fit side-chains outliers start: 55 outliers final: 13 residues processed: 275 average time/residue: 1.0684 time to fit residues: 327.7933 Evaluate side-chains 218 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.2162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 E 85 ASN F 108 HIS F 112 ASN G 85 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 14972 Z= 0.547 Angle : 0.743 11.733 20308 Z= 0.369 Chirality : 0.043 0.189 2312 Planarity : 0.005 0.039 2504 Dihedral : 14.085 107.304 2268 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.76 % Rotamer Outliers : 5.51 % 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: 0.28 (0.19), residues: 1872 helix: 0.95 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -2.53 (0.28), residues: 412 *********************** 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 282 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 213 time to evaluate : 1.761 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 23 residues processed: 262 average time/residue: 0.9214 time to fit residues: 273.3254 Evaluate side-chains 217 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 2.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 181 optimal weight: 50.0000 chunk 89 optimal weight: 50.0000 chunk 162 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 E 85 ASN G 85 ASN G 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14972 Z= 0.184 Angle : 0.578 9.540 20308 Z= 0.290 Chirality : 0.036 0.194 2312 Planarity : 0.004 0.053 2504 Dihedral : 11.830 85.726 2268 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.63 % Rotamer Outliers : 6.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1872 helix: 1.54 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 424 *********************** 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 294 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 217 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 22 residues processed: 263 average time/residue: 0.9794 time to fit residues: 289.9495 Evaluate side-chains 213 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 2.1978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 45 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 85 ASN B 108 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN E 125 GLN F 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 14972 Z= 0.410 Angle : 0.665 9.534 20308 Z= 0.332 Chirality : 0.040 0.378 2312 Planarity : 0.004 0.033 2504 Dihedral : 12.532 95.061 2268 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.79 % Favored : 95.99 % Rotamer Outliers : 4.95 % 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: 0.89 (0.19), residues: 1872 helix: 1.38 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 420 *********************** 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 261 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 199 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 28 residues processed: 241 average time/residue: 0.9120 time to fit residues: 249.3121 Evaluate side-chains 218 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.1572 time to fit residues: 2.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 35 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 85 ASN A 125 GLN B 108 HIS B 112 ASN C 85 ASN C 125 GLN E 85 ASN E 125 GLN F 108 HIS G 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 14972 Z= 0.310 Angle : 0.623 9.847 20308 Z= 0.311 Chirality : 0.037 0.306 2312 Planarity : 0.004 0.031 2504 Dihedral : 11.779 90.030 2268 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.47 % Favored : 96.31 % Rotamer Outliers : 5.11 % 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: 1.01 (0.19), residues: 1872 helix: 1.44 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -2.13 (0.30), residues: 412 *********************** 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 265 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 38 residues processed: 243 average time/residue: 0.9510 time to fit residues: 261.3225 Evaluate side-chains 233 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 9 average time/residue: 0.4616 time to fit residues: 7.4135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 50.0000 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 C 125 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 125 GLN F 108 HIS G 125 GLN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14972 Z= 0.184 Angle : 0.580 9.924 20308 Z= 0.289 Chirality : 0.036 0.386 2312 Planarity : 0.004 0.032 2504 Dihedral : 10.759 85.222 2268 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.53 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1872 helix: 1.73 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 416 *********************** 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 291 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 228 time to evaluate : 1.618 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 269 average time/residue: 0.8885 time to fit residues: 271.6593 Evaluate side-chains 224 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 4 average time/residue: 0.5545 time to fit residues: 4.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 16 optimal weight: 0.0670 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 B 112 ASN C 125 GLN D 108 HIS D 112 ASN E 77 HIS E 85 ASN E 125 GLN F 108 HIS F 112 ASN G 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14972 Z= 0.164 Angle : 0.585 11.158 20308 Z= 0.290 Chirality : 0.035 0.347 2312 Planarity : 0.004 0.030 2504 Dihedral : 10.309 85.422 2268 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.10 % Favored : 96.69 % Rotamer Outliers : 4.07 % 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: 1.58 (0.20), residues: 1872 helix: 1.90 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 424 *********************** 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 283 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 232 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 267 average time/residue: 0.9423 time to fit residues: 285.3682 Evaluate side-chains 225 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 2 average time/residue: 0.9201 time to fit residues: 4.3844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 178 optimal weight: 30.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 125 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 85 ASN E 125 GLN ** E 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS F 112 ASN G 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14972 Z= 0.200 Angle : 0.591 11.356 20308 Z= 0.293 Chirality : 0.037 0.402 2312 Planarity : 0.004 0.047 2504 Dihedral : 10.365 84.133 2268 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.83 % Favored : 96.96 % Rotamer Outliers : 3.12 % 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: 1.63 (0.20), residues: 1872 helix: 1.95 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.13 (0.30), residues: 420 *********************** 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 245 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 206 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 28 residues processed: 234 average time/residue: 0.8998 time to fit residues: 239.8452 Evaluate side-chains 222 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.1577 time to fit residues: 3.1878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B 112 ASN C 125 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 85 ASN ** E 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS F 112 ASN G 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14972 Z= 0.218 Angle : 0.602 11.216 20308 Z= 0.300 Chirality : 0.036 0.399 2312 Planarity : 0.004 0.046 2504 Dihedral : 10.554 85.365 2268 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.26 % Rotamer Outliers : 3.12 % 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: 1.62 (0.20), residues: 1872 helix: 1.93 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -2.12 (0.30), residues: 420 ********************** 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 242 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 233 average time/residue: 0.9492 time to fit residues: 250.4441 Evaluate side-chains 218 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.1754 time to fit residues: 3.0265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 41 optimal weight: 0.0060 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 8 optimal weight: 20.0000 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 C 125 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 85 ASN ** E 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.254728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144030 restraints weight = 15344.385| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.59 r_work: 0.3279 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14972 Z= 0.211 Angle : 0.603 10.486 20308 Z= 0.301 Chirality : 0.037 0.423 2312 Planarity : 0.004 0.036 2504 Dihedral : 10.538 85.378 2268 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.83 % Favored : 96.96 % Rotamer Outliers : 2.64 % 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: 1.62 (0.20), residues: 1872 helix: 1.92 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 412 =============================================================================== Job complete usr+sys time: 5359.45 seconds wall clock time: 95 minutes 51.83 seconds (5751.83 seconds total)