Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 12:14:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/04_2023/7tcp_25816.pdb" } resolution = 3.84 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= 0.008 sd= 0.017 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: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 68 5.16 5 C 9724 2.51 5 N 2572 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14992 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2711 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1034 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2711 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1034 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2711 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1034 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2711 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1034 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 Time building chain proxies: 8.11, per 1000 atoms: 0.54 Number of scatterers: 14992 At special positions: 0 Unit cell: (102.93, 102.93, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 68 16.00 O 2616 8.00 N 2572 7.00 C 9724 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: 6.80 Conformation dependent library (CDL) restraints added in 2.4 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 81.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 110 through 135 removed outlier: 3.763A pdb=" N ILE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 4.216A pdb=" N THR A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.688A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.561A pdb=" N ASP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 233 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 234' Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.836A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.583A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 removed outlier: 4.117A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.793A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.777A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.662A pdb=" N GLU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.605A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 110 through 135 removed outlier: 3.764A pdb=" N ILE E 135 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 168 removed outlier: 4.218A pdb=" N THR E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.756A pdb=" N ARG E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 205 Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.562A pdb=" N ASP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG E 233 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN E 234 " --> pdb=" O VAL E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 234' Processing helix chain 'E' and resid 235 through 248 removed outlier: 3.837A pdb=" N LEU E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.553A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 274 removed outlier: 4.123A pdb=" N PHE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 300 Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.795A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 356 Processing helix chain 'E' and resid 357 through 375 removed outlier: 3.778A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA E 502 " --> pdb=" O HIS E 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL E 505 " --> pdb=" O ALA E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 11 through 22 removed outlier: 3.657A pdb=" N GLU F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.606A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 110 through 135 removed outlier: 3.763A pdb=" N ILE G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 168 removed outlier: 4.218A pdb=" N THR G 143 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 175 through 185 removed outlier: 3.737A pdb=" N ARG G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 205 Processing helix chain 'G' and resid 219 through 228 Processing helix chain 'G' and resid 229 through 234 removed outlier: 3.561A pdb=" N ASP G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG G 233 " --> pdb=" O HIS G 230 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN G 234 " --> pdb=" O VAL G 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 234' Processing helix chain 'G' and resid 235 through 248 removed outlier: 3.837A pdb=" N LEU G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.579A pdb=" N ILE G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 274 removed outlier: 4.121A pdb=" N PHE G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 300 Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.793A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 349 Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 356 Processing helix chain 'G' and resid 357 through 375 removed outlier: 3.779A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 removed outlier: 3.800A pdb=" N ALA G 502 " --> pdb=" O HIS G 498 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL G 505 " --> pdb=" O ALA G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 11 through 22 removed outlier: 3.659A pdb=" N GLU H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.603A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.806A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.764A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 168 removed outlier: 4.216A pdb=" N THR C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.688A pdb=" N ARG C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 205 Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.562A pdb=" N ASP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG C 233 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN C 234 " --> pdb=" O VAL C 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 234' Processing helix chain 'C' and resid 235 through 248 removed outlier: 3.836A pdb=" N LEU C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.553A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 removed outlier: 4.119A pdb=" N PHE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.796A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 349 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 375 removed outlier: 3.778A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 removed outlier: 3.796A pdb=" N ALA C 502 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.659A pdb=" N GLU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.605A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 94 removed outlier: 3.801A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.502A pdb=" N ILE B 64 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.500A pdb=" N ILE F 64 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.502A pdb=" N ILE H 64 " --> pdb=" O ILE H 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 102 1066 hydrogen bonds defined for protein. 3183 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: 4.39 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4804 1.34 - 1.46: 3672 1.46 - 1.58: 6712 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15304 Sorted by residual: bond pdb=" CA VAL G 300 " pdb=" C VAL G 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.72e-01 bond pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.30e-01 bond pdb=" CA VAL E 300 " pdb=" C VAL E 300 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.26e-02 6.30e+03 6.24e-01 bond pdb=" CA VAL C 300 " pdb=" C VAL C 300 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.26e-02 6.30e+03 5.68e-01 bond pdb=" CA VAL C 300 " pdb=" CB VAL C 300 " ideal model delta sigma weight residual 1.542 1.534 0.008 1.28e-02 6.10e+03 4.08e-01 ... (remaining 15299 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 268 107.04 - 113.78: 8509 113.78 - 120.51: 6283 120.51 - 127.25: 5512 127.25 - 133.99: 148 Bond angle restraints: 20720 Sorted by residual: angle pdb=" C GLU A 105 " pdb=" N ARG A 106 " pdb=" CA ARG A 106 " ideal model delta sigma weight residual 121.80 126.68 -4.88 2.44e+00 1.68e-01 4.00e+00 angle pdb=" C GLU G 105 " pdb=" N ARG G 106 " pdb=" CA ARG G 106 " ideal model delta sigma weight residual 121.80 126.67 -4.87 2.44e+00 1.68e-01 3.98e+00 angle pdb=" C GLU E 105 " pdb=" N ARG E 106 " pdb=" CA ARG E 106 " ideal model delta sigma weight residual 121.80 126.66 -4.86 2.44e+00 1.68e-01 3.97e+00 angle pdb=" C GLU C 105 " pdb=" N ARG C 106 " pdb=" CA ARG C 106 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" CA ARG G 106 " pdb=" CB ARG G 106 " pdb=" CG ARG G 106 " ideal model delta sigma weight residual 114.10 117.69 -3.59 2.00e+00 2.50e-01 3.23e+00 ... (remaining 20715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 8463 15.61 - 31.23: 384 31.23 - 46.84: 63 46.84 - 62.46: 18 62.46 - 78.07: 4 Dihedral angle restraints: 8932 sinusoidal: 3408 harmonic: 5524 Sorted by residual: dihedral pdb=" N PHE A 322 " pdb=" CA PHE A 322 " pdb=" CB PHE A 322 " pdb=" CG PHE A 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.70 -49.70 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N PHE G 322 " pdb=" CA PHE G 322 " pdb=" CB PHE G 322 " pdb=" CG PHE G 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.67 -49.67 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N PHE C 322 " pdb=" CA PHE C 322 " pdb=" CB PHE C 322 " pdb=" CG PHE C 322 " ideal model delta sinusoidal sigma weight residual 60.00 109.66 -49.66 3 1.50e+01 4.44e-03 8.80e+00 ... (remaining 8929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1388 0.023 - 0.047: 530 0.047 - 0.070: 304 0.070 - 0.093: 67 0.093 - 0.117: 51 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CA ILE D 101 " pdb=" N ILE D 101 " pdb=" C ILE D 101 " pdb=" CB ILE D 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE H 101 " pdb=" N ILE H 101 " pdb=" C ILE H 101 " pdb=" CB ILE H 101 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 2337 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 298 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.91e-01 pdb=" C VAL E 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL E 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR E 299 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 298 " -0.005 2.00e-02 2.50e+03 9.22e-03 8.50e-01 pdb=" C VAL G 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL G 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR G 299 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 298 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 298 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 298 " -0.006 2.00e-02 2.50e+03 pdb=" N THR C 299 " -0.005 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5011 2.84 - 3.36: 15741 3.36 - 3.87: 24497 3.87 - 4.39: 26433 4.39 - 4.90: 46762 Nonbonded interactions: 118444 Sorted by model distance: nonbonded pdb=" OG1 THR A 299 " pdb=" OH TYR G 305 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR A 305 " pdb=" OG1 THR C 299 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR E 305 " pdb=" OG1 THR G 299 " model vdw 2.329 2.440 nonbonded pdb=" OG1 THR E 299 " pdb=" OH TYR C 305 " model vdw 2.335 2.440 nonbonded pdb=" O VAL A 297 " pdb=" OG1 THR A 301 " model vdw 2.343 2.440 ... (remaining 118439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 12.620 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 39.880 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.002 0.018 15304 Z= 0.114 Angle : 0.375 6.039 20720 Z= 0.202 Chirality : 0.035 0.117 2340 Planarity : 0.002 0.023 2604 Dihedral : 9.569 78.072 5372 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.26 % 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: 2.66 (0.20), residues: 1880 helix: 2.57 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.80 (0.31), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.993 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2537 time to fit residues: 62.2260 Evaluate side-chains 113 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1380 time to fit residues: 6.3009 ------------------------------------------------------------------------------- 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: 7.9990 chunk 142 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 15304 Z= 0.139 Angle : 0.424 6.005 20720 Z= 0.228 Chirality : 0.036 0.122 2340 Planarity : 0.002 0.019 2604 Dihedral : 2.914 10.040 2080 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.93 % 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: 2.55 (0.20), residues: 1880 helix: 2.48 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.892 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 124 average time/residue: 0.2065 time to fit residues: 43.8425 Evaluate side-chains 105 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1312 time to fit residues: 5.8361 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.036 15304 Z= 0.372 Angle : 0.542 7.213 20720 Z= 0.290 Chirality : 0.040 0.131 2340 Planarity : 0.003 0.020 2604 Dihedral : 3.248 12.613 2080 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 1.66 % 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: 1.83 (0.19), residues: 1880 helix: 1.99 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.965 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.2041 time to fit residues: 39.6704 Evaluate side-chains 104 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1338 time to fit residues: 6.4386 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 15304 Z= 0.132 Angle : 0.412 6.046 20720 Z= 0.220 Chirality : 0.035 0.115 2340 Planarity : 0.002 0.018 2604 Dihedral : 3.091 10.545 2080 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 2.06 % 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: 2.20 (0.20), residues: 1880 helix: 2.21 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.968 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 121 average time/residue: 0.2060 time to fit residues: 42.6696 Evaluate side-chains 104 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1317 time to fit residues: 5.6414 ------------------------------------------------------------------------------- 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: 1.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 15304 Z= 0.177 Angle : 0.436 6.303 20720 Z= 0.230 Chirality : 0.036 0.114 2340 Planarity : 0.002 0.018 2604 Dihedral : 3.054 10.920 2080 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 1.60 % 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: 2.33 (0.20), residues: 1880 helix: 2.32 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.23 (0.32), residues: 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.919 Fit side-chains outliers start: 24 outliers final: 4 residues processed: 113 average time/residue: 0.2147 time to fit residues: 41.2916 Evaluate side-chains 96 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1313 time to fit residues: 3.5538 ------------------------------------------------------------------------------- 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: 3.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 15304 Z= 0.192 Angle : 0.439 6.292 20720 Z= 0.232 Chirality : 0.036 0.116 2340 Planarity : 0.002 0.018 2604 Dihedral : 3.101 11.452 2080 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.80 % 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: 2.27 (0.20), residues: 1880 helix: 2.30 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.36 (0.31), residues: 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 1.968 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 107 average time/residue: 0.2095 time to fit residues: 38.1464 Evaluate side-chains 107 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1209 time to fit residues: 5.8110 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.0970 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 15304 Z= 0.143 Angle : 0.419 6.320 20720 Z= 0.221 Chirality : 0.035 0.116 2340 Planarity : 0.002 0.019 2604 Dihedral : 3.020 10.747 2080 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.73 % 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: 2.39 (0.20), residues: 1880 helix: 2.35 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.19 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.894 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 107 average time/residue: 0.2097 time to fit residues: 38.4369 Evaluate side-chains 101 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1318 time to fit residues: 3.5103 ------------------------------------------------------------------------------- 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: 0.7980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 164 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 15304 Z= 0.116 Angle : 0.417 8.016 20720 Z= 0.216 Chirality : 0.035 0.118 2340 Planarity : 0.002 0.020 2604 Dihedral : 2.931 10.586 2080 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.93 % 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: 2.53 (0.20), residues: 1880 helix: 2.45 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.918 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 0.2076 time to fit residues: 39.2196 Evaluate side-chains 107 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1336 time to fit residues: 5.1476 ------------------------------------------------------------------------------- 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: 6.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15304 Z= 0.115 Angle : 0.410 9.186 20720 Z= 0.214 Chirality : 0.035 0.118 2340 Planarity : 0.002 0.021 2604 Dihedral : 2.872 10.407 2080 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.33 % 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: 2.63 (0.20), residues: 1880 helix: 2.52 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.13 (0.32), residues: 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.906 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 0.2307 time to fit residues: 41.2145 Evaluate side-chains 98 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1234 time to fit residues: 2.6551 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.0010 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 15304 Z= 0.163 Angle : 0.453 10.213 20720 Z= 0.230 Chirality : 0.036 0.117 2340 Planarity : 0.002 0.020 2604 Dihedral : 2.893 10.878 2080 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.33 % 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: 2.60 (0.20), residues: 1880 helix: 2.50 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.712 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.2096 time to fit residues: 36.0816 Evaluate side-chains 101 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1326 time to fit residues: 3.8800 ------------------------------------------------------------------------------- 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: 3.9990 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.125359 restraints weight = 26753.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.120755 restraints weight = 42838.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.119848 restraints weight = 41496.903| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15304 Z= 0.183 Angle : 0.468 12.215 20720 Z= 0.237 Chirality : 0.036 0.116 2340 Planarity : 0.002 0.020 2604 Dihedral : 2.946 11.205 2080 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.40 % 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: 2.52 (0.20), residues: 1880 helix: 2.44 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 428 =============================================================================== Job complete usr+sys time: 2201.17 seconds wall clock time: 41 minutes 54.15 seconds (2514.15 seconds total)