Starting phenix.real_space_refine on Sat Mar 16 15:26:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/03_2024/7tcp_25816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/03_2024/7tcp_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_25816/03_2024/7tcp_25816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/03_2024/7tcp_25816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/03_2024/7tcp_25816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcp_25816/03_2024/7tcp_25816.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.86, per 1000 atoms: 0.52 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: 5.64 Conformation dependent library (CDL) restraints added in 2.7 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: 1.57 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: 4.28 Time building geometry restraints manager: 6.05 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: 3.500 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: 12.180 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.760 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.480 ------------------------------------------------------------------------------- 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 % Allowed : 3.32 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 369 HIS 0.001 0.000 HIS G 353 PHE 0.005 0.001 PHE B 17 TYR 0.011 0.001 TYR E 534 ARG 0.002 0.000 ARG C 227 *********************** 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 : 1.771 Fit side-chains REVERT: B 118 THR cc_start: 0.8536 (p) cc_final: 0.8299 (m) REVERT: F 118 THR cc_start: 0.8559 (p) cc_final: 0.8293 (m) REVERT: H 118 THR cc_start: 0.8541 (p) cc_final: 0.8290 (m) REVERT: D 118 THR cc_start: 0.8541 (p) cc_final: 0.8291 (m) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2210 time to fit residues: 53.7943 Evaluate side-chains 113 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL 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: 0.7870 moved from start: 0.0768 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= 0.136 Angle : 0.417 5.991 20720 Z= 0.223 Chirality : 0.036 0.122 2340 Planarity : 0.002 0.019 2604 Dihedral : 4.636 52.833 2099 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.33 % Allowed : 6.52 % Favored : 91.16 % 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: 1432 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 369 HIS 0.006 0.001 HIS D 108 PHE 0.018 0.001 PHE F 93 TYR 0.012 0.001 TYR C 534 ARG 0.004 0.000 ARG H 127 *********************** 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 147 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 1.761 Fit side-chains REVERT: B 118 THR cc_start: 0.8499 (p) cc_final: 0.8261 (m) REVERT: F 118 THR cc_start: 0.8529 (p) cc_final: 0.8268 (m) REVERT: H 118 THR cc_start: 0.8518 (p) cc_final: 0.8281 (m) REVERT: D 118 THR cc_start: 0.8519 (p) cc_final: 0.8264 (m) outliers start: 35 outliers final: 23 residues processed: 131 average time/residue: 0.1994 time to fit residues: 44.5127 Evaluate side-chains 119 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 0.0000 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15304 Z= 0.357 Angle : 0.533 7.249 20720 Z= 0.284 Chirality : 0.039 0.130 2340 Planarity : 0.003 0.019 2604 Dihedral : 4.812 55.129 2098 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 6.32 % Favored : 90.29 % 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: 1.86 (0.20), residues: 1880 helix: 2.00 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 369 HIS 0.004 0.001 HIS D 108 PHE 0.027 0.002 PHE D 93 TYR 0.019 0.002 TYR G 534 ARG 0.003 0.001 ARG C 227 *********************** 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 151 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 100 time to evaluate : 1.851 Fit side-chains REVERT: F 118 THR cc_start: 0.8612 (p) cc_final: 0.8406 (m) outliers start: 51 outliers final: 40 residues processed: 131 average time/residue: 0.2001 time to fit residues: 44.5067 Evaluate side-chains 131 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 91 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0870 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.1227 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= 0.122 Angle : 0.411 6.149 20720 Z= 0.219 Chirality : 0.035 0.115 2340 Planarity : 0.002 0.018 2604 Dihedral : 4.645 53.879 2098 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.93 % Allowed : 7.65 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.20), residues: 1880 helix: 2.23 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 369 HIS 0.004 0.001 HIS H 108 PHE 0.022 0.001 PHE F 93 TYR 0.012 0.001 TYR C 534 ARG 0.002 0.000 ARG B 107 *********************** 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 146 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 102 time to evaluate : 1.852 Fit side-chains outliers start: 44 outliers final: 26 residues processed: 126 average time/residue: 0.1987 time to fit residues: 42.7588 Evaluate side-chains 122 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.1315 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= 0.153 Angle : 0.426 6.171 20720 Z= 0.223 Chirality : 0.036 0.114 2340 Planarity : 0.002 0.018 2604 Dihedral : 4.504 54.550 2096 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.12 % Allowed : 6.98 % Favored : 89.89 % 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: 2.34 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 369 HIS 0.004 0.001 HIS F 108 PHE 0.007 0.001 PHE F 93 TYR 0.013 0.001 TYR C 534 ARG 0.002 0.000 ARG G 227 *********************** 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 160 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 1.753 Fit side-chains outliers start: 47 outliers final: 30 residues processed: 138 average time/residue: 0.1953 time to fit residues: 45.8274 Evaluate side-chains 130 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15304 Z= 0.127 Angle : 0.407 5.878 20720 Z= 0.214 Chirality : 0.035 0.114 2340 Planarity : 0.002 0.019 2604 Dihedral : 4.511 54.335 2096 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 8.58 % Favored : 89.16 % 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: 2.51 (0.20), residues: 1880 helix: 2.43 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.14 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 369 HIS 0.003 0.001 HIS D 108 PHE 0.010 0.001 PHE H 93 TYR 0.011 0.001 TYR C 534 ARG 0.001 0.000 ARG C 233 *********************** 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 143 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.952 Fit side-chains outliers start: 34 outliers final: 30 residues processed: 118 average time/residue: 0.2042 time to fit residues: 40.8053 Evaluate side-chains 133 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 153 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.1478 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= 0.112 Angle : 0.410 6.846 20720 Z= 0.212 Chirality : 0.035 0.115 2340 Planarity : 0.002 0.020 2604 Dihedral : 4.456 54.330 2096 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.93 % Allowed : 8.84 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.20), residues: 1880 helix: 2.53 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 369 HIS 0.003 0.001 HIS D 108 PHE 0.016 0.001 PHE D 93 TYR 0.010 0.001 TYR C 534 ARG 0.001 0.000 ARG E 233 *********************** 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 139 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.709 Fit side-chains outliers start: 29 outliers final: 29 residues processed: 119 average time/residue: 0.1994 time to fit residues: 40.1582 Evaluate side-chains 130 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15304 Z= 0.309 Angle : 0.515 6.877 20720 Z= 0.272 Chirality : 0.039 0.125 2340 Planarity : 0.003 0.018 2604 Dihedral : 4.657 56.111 2096 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 9.04 % Favored : 88.03 % 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: 2.18 (0.20), residues: 1880 helix: 2.19 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 369 HIS 0.005 0.001 HIS C 230 PHE 0.012 0.001 PHE H 93 TYR 0.019 0.002 TYR C 534 ARG 0.003 0.000 ARG E 227 *********************** 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 148 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 104 time to evaluate : 1.789 Fit side-chains REVERT: A 509 MET cc_start: 0.8449 (mtt) cc_final: 0.8092 (mtt) REVERT: E 509 MET cc_start: 0.8623 (mtt) cc_final: 0.8299 (mtt) REVERT: G 509 MET cc_start: 0.8573 (mtt) cc_final: 0.8249 (mtt) REVERT: C 509 MET cc_start: 0.8497 (mtt) cc_final: 0.8161 (mtt) outliers start: 44 outliers final: 37 residues processed: 126 average time/residue: 0.1930 time to fit residues: 41.3999 Evaluate side-chains 137 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 4.9990 chunk 158 optimal weight: 0.0170 chunk 168 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 152 optimal weight: 0.0570 chunk 159 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.1549 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= 0.113 Angle : 0.418 5.838 20720 Z= 0.218 Chirality : 0.035 0.117 2340 Planarity : 0.002 0.020 2604 Dihedral : 4.547 54.397 2096 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 10.44 % Favored : 87.83 % 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: 2.54 (0.20), residues: 1880 helix: 2.47 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.14 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 369 HIS 0.002 0.001 HIS C 499 PHE 0.007 0.001 PHE H 93 TYR 0.010 0.001 TYR C 534 ARG 0.001 0.000 ARG G 370 *********************** 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 130 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.810 Fit side-chains REVERT: E 509 MET cc_start: 0.8497 (mtt) cc_final: 0.8161 (mtt) REVERT: G 509 MET cc_start: 0.8469 (mtt) cc_final: 0.8084 (mtt) outliers start: 26 outliers final: 25 residues processed: 113 average time/residue: 0.2003 time to fit residues: 38.6565 Evaluate side-chains 129 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15304 Z= 0.134 Angle : 0.417 5.884 20720 Z= 0.218 Chirality : 0.035 0.117 2340 Planarity : 0.002 0.019 2604 Dihedral : 4.481 54.893 2096 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.13 % Allowed : 10.24 % Favored : 87.63 % 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: 2.62 (0.20), residues: 1880 helix: 2.53 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 369 HIS 0.001 0.000 HIS C 230 PHE 0.009 0.001 PHE F 93 TYR 0.012 0.001 TYR C 534 ARG 0.001 0.000 ARG G 233 ********************** 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 137 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.799 Fit side-chains REVERT: A 509 MET cc_start: 0.8591 (mtt) cc_final: 0.8287 (mtt) REVERT: B 70 LEU cc_start: 0.8222 (mt) cc_final: 0.7935 (mp) REVERT: F 70 LEU cc_start: 0.8293 (mt) cc_final: 0.7968 (mp) REVERT: G 509 MET cc_start: 0.8492 (mtt) cc_final: 0.8107 (mtt) REVERT: H 70 LEU cc_start: 0.8202 (mt) cc_final: 0.7896 (mp) REVERT: D 70 LEU cc_start: 0.8243 (mt) cc_final: 0.7943 (mp) outliers start: 32 outliers final: 29 residues processed: 116 average time/residue: 0.2029 time to fit residues: 39.6802 Evaluate side-chains 133 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.121083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118103 restraints weight = 27183.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116975 restraints weight = 41149.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116543 restraints weight = 52906.984| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15304 Z= 0.384 Angle : 0.576 8.844 20720 Z= 0.302 Chirality : 0.040 0.159 2340 Planarity : 0.003 0.021 2604 Dihedral : 4.784 56.652 2096 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.46 % Allowed : 9.91 % Favored : 87.63 % 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: 1.97 (0.19), residues: 1880 helix: 2.10 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 369 HIS 0.006 0.001 HIS C 230 PHE 0.012 0.002 PHE B 90 TYR 0.021 0.002 TYR C 534 ARG 0.004 0.000 ARG G 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.61 seconds wall clock time: 42 minutes 46.46 seconds (2566.46 seconds total)