Starting phenix.real_space_refine on Wed Feb 21 06:44:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd6_15976/02_2024/8bd6_15976_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 338 5.49 5 Mg 9 5.21 5 S 85 5.16 5 C 17646 2.51 5 N 5416 2.21 5 O 6457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29951 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4542 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 17, 'TRANS': 542} Chain breaks: 2 Chain: "B" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 4961 Classifications: {'RNA': 233} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 16, 'rna3p_pur': 102, 'rna3p_pyr': 97} Link IDs: {'rna2p': 34, 'rna3p': 198} Chain breaks: 1 Chain: "C" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 356 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Z" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "c" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "d" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.91, per 1000 atoms: 0.53 Number of scatterers: 29951 At special positions: 0 Unit cell: (149.5, 133.9, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 338 15.00 Mg 9 11.99 O 6457 8.00 N 5416 7.00 C 17646 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: 14.38 Conformation dependent library (CDL) restraints added in 4.4 seconds 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 12 sheets defined 54.3% alpha, 5.9% beta 101 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 13.08 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 removed outlier: 3.830A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.270A pdb=" N GLU A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.508A pdb=" N CYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 77 through 114 Processing helix chain 'A' and resid 118 through 124 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 319 through 337 removed outlier: 4.400A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 384 through 406 removed outlier: 3.669A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.584A pdb=" N GLN A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'A' and resid 485 through 505 Processing helix chain 'A' and resid 519 through 537 removed outlier: 3.662A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 553 through 566 Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 619 through 635 Processing helix chain 'R' and resid 18 through 29 Processing helix chain 'R' and resid 37 through 51 Processing helix chain 'R' and resid 66 through 76 Processing helix chain 'R' and resid 102 through 112 Processing helix chain 'R' and resid 122 through 135 Processing helix chain 'R' and resid 151 through 164 removed outlier: 4.136A pdb=" N ALA R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 181 Processing helix chain 'R' and resid 185 through 189 Processing helix chain 'R' and resid 202 through 214 Processing helix chain 'R' and resid 227 through 237 Processing helix chain 'R' and resid 241 through 257 Processing helix chain 'R' and resid 265 through 273 Processing helix chain 'S' and resid 18 through 29 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 66 through 76 Processing helix chain 'S' and resid 102 through 112 Processing helix chain 'S' and resid 122 through 135 Processing helix chain 'S' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA S 155 " --> pdb=" O PRO S 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP S 156 " --> pdb=" O GLU S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 181 Processing helix chain 'S' and resid 185 through 189 Processing helix chain 'S' and resid 202 through 214 Processing helix chain 'S' and resid 227 through 237 Processing helix chain 'S' and resid 241 through 257 Processing helix chain 'S' and resid 265 through 273 Processing helix chain 'T' and resid 18 through 29 Processing helix chain 'T' and resid 37 through 51 Processing helix chain 'T' and resid 66 through 76 Processing helix chain 'T' and resid 102 through 112 Processing helix chain 'T' and resid 122 through 135 Processing helix chain 'T' and resid 151 through 164 removed outlier: 4.139A pdb=" N ALA T 155 " --> pdb=" O PRO T 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 181 Processing helix chain 'T' and resid 185 through 189 Processing helix chain 'T' and resid 202 through 214 Processing helix chain 'T' and resid 227 through 237 Processing helix chain 'T' and resid 241 through 257 Processing helix chain 'T' and resid 265 through 273 Processing helix chain 'U' and resid 18 through 29 Processing helix chain 'U' and resid 37 through 51 Processing helix chain 'U' and resid 66 through 76 Processing helix chain 'U' and resid 102 through 112 Processing helix chain 'U' and resid 122 through 135 Processing helix chain 'U' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA U 155 " --> pdb=" O PRO U 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP U 156 " --> pdb=" O GLU U 152 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 181 Processing helix chain 'U' and resid 185 through 189 Processing helix chain 'U' and resid 202 through 214 Processing helix chain 'U' and resid 227 through 237 Processing helix chain 'U' and resid 241 through 257 removed outlier: 3.864A pdb=" N GLU U 246 " --> pdb=" O GLY U 242 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 273 Processing helix chain 'V' and resid 18 through 29 Processing helix chain 'V' and resid 37 through 51 Processing helix chain 'V' and resid 66 through 76 Processing helix chain 'V' and resid 102 through 112 Processing helix chain 'V' and resid 122 through 135 Processing helix chain 'V' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA V 155 " --> pdb=" O PRO V 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP V 156 " --> pdb=" O GLU V 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 181 Processing helix chain 'V' and resid 185 through 189 Processing helix chain 'V' and resid 202 through 214 Processing helix chain 'V' and resid 227 through 237 Processing helix chain 'V' and resid 241 through 257 Processing helix chain 'V' and resid 265 through 273 Processing helix chain 'W' and resid 18 through 29 Processing helix chain 'W' and resid 37 through 51 Processing helix chain 'W' and resid 66 through 76 Processing helix chain 'W' and resid 102 through 112 Processing helix chain 'W' and resid 122 through 135 Processing helix chain 'W' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA W 155 " --> pdb=" O PRO W 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP W 156 " --> pdb=" O GLU W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 181 Processing helix chain 'W' and resid 185 through 189 Processing helix chain 'W' and resid 202 through 214 Processing helix chain 'W' and resid 227 through 237 Processing helix chain 'W' and resid 241 through 257 Processing helix chain 'W' and resid 265 through 273 Processing helix chain 'X' and resid 18 through 29 Processing helix chain 'X' and resid 37 through 51 Processing helix chain 'X' and resid 66 through 76 Processing helix chain 'X' and resid 102 through 112 Processing helix chain 'X' and resid 122 through 135 Processing helix chain 'X' and resid 151 through 164 removed outlier: 4.139A pdb=" N ALA X 155 " --> pdb=" O PRO X 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP X 156 " --> pdb=" O GLU X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 181 Processing helix chain 'X' and resid 185 through 189 Processing helix chain 'X' and resid 202 through 214 Processing helix chain 'X' and resid 227 through 237 Processing helix chain 'X' and resid 241 through 257 Processing helix chain 'X' and resid 265 through 273 Processing helix chain 'Y' and resid 18 through 29 Processing helix chain 'Y' and resid 37 through 51 Processing helix chain 'Y' and resid 66 through 76 Processing helix chain 'Y' and resid 102 through 112 Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'Y' and resid 151 through 164 removed outlier: 4.139A pdb=" N ALA Y 155 " --> pdb=" O PRO Y 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP Y 156 " --> pdb=" O GLU Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 181 Processing helix chain 'Y' and resid 185 through 189 Processing helix chain 'Y' and resid 202 through 214 Processing helix chain 'Y' and resid 227 through 237 Processing helix chain 'Y' and resid 241 through 257 Processing helix chain 'Y' and resid 265 through 273 Processing helix chain 'Z' and resid 18 through 29 Processing helix chain 'Z' and resid 37 through 51 Processing helix chain 'Z' and resid 66 through 76 Processing helix chain 'Z' and resid 102 through 112 Processing helix chain 'Z' and resid 122 through 135 Processing helix chain 'Z' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA Z 155 " --> pdb=" O PRO Z 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP Z 156 " --> pdb=" O GLU Z 152 " (cutoff:3.500A) Processing helix chain 'Z' and resid 174 through 182 removed outlier: 3.763A pdb=" N ARG Z 182 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 189 No H-bonds generated for 'chain 'Z' and resid 186 through 189' Processing helix chain 'Z' and resid 202 through 214 Processing helix chain 'Z' and resid 227 through 237 Processing helix chain 'Z' and resid 241 through 257 Processing helix chain 'Z' and resid 265 through 273 Processing sheet with id= A, first strand: chain 'A' and resid 314 through 316 removed outlier: 4.719A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 607 through 611 removed outlier: 7.604A pdb=" N LEU A 453 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 448 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 464 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL R 58 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU R 170 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL S 58 " --> pdb=" O VAL S 168 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU S 170 " --> pdb=" O VAL S 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL T 58 " --> pdb=" O VAL T 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU T 170 " --> pdb=" O VAL T 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'U' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL U 58 " --> pdb=" O VAL U 168 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU U 170 " --> pdb=" O VAL U 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'V' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL V 58 " --> pdb=" O VAL V 168 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU V 170 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL W 58 " --> pdb=" O VAL W 168 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU W 170 " --> pdb=" O VAL W 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'X' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL X 58 " --> pdb=" O VAL X 168 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU X 170 " --> pdb=" O VAL X 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Y' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL Y 58 " --> pdb=" O VAL Y 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU Y 170 " --> pdb=" O VAL Y 58 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Z' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL Z 58 " --> pdb=" O VAL Z 168 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU Z 170 " --> pdb=" O VAL Z 58 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 254 hydrogen bonds 464 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 11.76 Time building geometry restraints manager: 15.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4224 1.30 - 1.43: 9119 1.43 - 1.55: 16921 1.55 - 1.68: 698 1.68 - 1.81: 127 Bond restraints: 31089 Sorted by residual: bond pdb=" CA LEU A 368 " pdb=" C LEU A 368 " ideal model delta sigma weight residual 1.521 1.464 0.057 9.90e-03 1.02e+04 3.28e+01 bond pdb=" C GLY T 242 " pdb=" O GLY T 242 " ideal model delta sigma weight residual 1.234 1.173 0.062 1.19e-02 7.06e+03 2.68e+01 bond pdb=" C GLY Z 242 " pdb=" O GLY Z 242 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.21e-02 6.83e+03 2.59e+01 bond pdb=" C GLY S 242 " pdb=" O GLY S 242 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ILE T 241 " pdb=" N GLY T 242 " ideal model delta sigma weight residual 1.334 1.274 0.060 1.21e-02 6.83e+03 2.42e+01 ... (remaining 31084 not shown) Histogram of bond angle deviations from ideal: 94.64 - 102.56: 701 102.56 - 110.47: 10716 110.47 - 118.39: 15570 118.39 - 126.31: 15213 126.31 - 134.23: 1233 Bond angle restraints: 43433 Sorted by residual: angle pdb=" N LEU Y 244 " pdb=" CA LEU Y 244 " pdb=" C LEU Y 244 " ideal model delta sigma weight residual 111.14 100.42 10.72 1.08e+00 8.57e-01 9.86e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 111.14 100.44 10.70 1.08e+00 8.57e-01 9.82e+01 angle pdb=" N PHE T 204 " pdb=" CA PHE T 204 " pdb=" C PHE T 204 " ideal model delta sigma weight residual 111.36 101.94 9.42 1.09e+00 8.42e-01 7.47e+01 angle pdb=" N PHE Z 204 " pdb=" CA PHE Z 204 " pdb=" C PHE Z 204 " ideal model delta sigma weight residual 111.36 101.95 9.41 1.09e+00 8.42e-01 7.45e+01 angle pdb=" N PHE S 204 " pdb=" CA PHE S 204 " pdb=" C PHE S 204 " ideal model delta sigma weight residual 111.36 101.96 9.40 1.09e+00 8.42e-01 7.44e+01 ... (remaining 43428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 17404 35.99 - 71.97: 1814 71.97 - 107.96: 118 107.96 - 143.94: 4 143.94 - 179.93: 8 Dihedral angle restraints: 19348 sinusoidal: 10926 harmonic: 8422 Sorted by residual: dihedral pdb=" O4' U B 23 " pdb=" C1' U B 23 " pdb=" N1 U B 23 " pdb=" C2 U B 23 " ideal model delta sinusoidal sigma weight residual -128.00 51.93 -179.93 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 129 " pdb=" C1' U B 129 " pdb=" N1 U B 129 " pdb=" C2 U B 129 " ideal model delta sinusoidal sigma weight residual -128.00 51.34 -179.34 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 138 " pdb=" C1' U B 138 " pdb=" N1 U B 138 " pdb=" C2 U B 138 " ideal model delta sinusoidal sigma weight residual 232.00 54.90 177.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4010 0.103 - 0.205: 801 0.205 - 0.308: 215 0.308 - 0.411: 19 0.411 - 0.513: 20 Chirality restraints: 5065 Sorted by residual: chirality pdb=" CA ARG R 76 " pdb=" N ARG R 76 " pdb=" C ARG R 76 " pdb=" CB ARG R 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA ARG S 76 " pdb=" N ARG S 76 " pdb=" C ARG S 76 " pdb=" CB ARG S 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA ARG Z 76 " pdb=" N ARG Z 76 " pdb=" C ARG Z 76 " pdb=" CB ARG Z 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 5062 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE U 241 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C ILE U 241 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE U 241 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY U 242 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY W 242 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C GLY W 242 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY W 242 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG W 243 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP V 301 " 0.063 2.00e-02 2.50e+03 2.75e-02 2.07e+01 pdb=" C2 ATP V 301 " -0.033 2.00e-02 2.50e+03 pdb=" C4 ATP V 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5 ATP V 301 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ATP V 301 " 0.028 2.00e-02 2.50e+03 pdb=" C8 ATP V 301 " -0.021 2.00e-02 2.50e+03 pdb=" N1 ATP V 301 " 0.006 2.00e-02 2.50e+03 pdb=" N3 ATP V 301 " -0.004 2.00e-02 2.50e+03 pdb=" N6 ATP V 301 " 0.024 2.00e-02 2.50e+03 pdb=" N7 ATP V 301 " -0.015 2.00e-02 2.50e+03 pdb=" N9 ATP V 301 " -0.033 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 17 1.83 - 2.60: 428 2.60 - 3.36: 39353 3.36 - 4.13: 80783 4.13 - 4.90: 132674 Nonbonded interactions: 253255 Sorted by model distance: nonbonded pdb=" CE1 HIS A 500 " pdb=" O2 U B 117 " model vdw 1.062 3.260 nonbonded pdb=" ND1 HIS A 500 " pdb=" O2 U B 117 " model vdw 1.086 2.520 nonbonded pdb=" CG2 ILE A 97 " pdb=" O2' G B 236 " model vdw 1.119 3.460 nonbonded pdb=" NE2 GLN A 513 " pdb=" C5' DT C -9 " model vdw 1.142 3.520 nonbonded pdb=" O1B ATP R 301 " pdb="MG MG R 302 " model vdw 1.185 2.170 ... (remaining 253250 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 'R' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = chain 'S' selection = (chain 'T' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'U' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'V' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'W' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'X' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'Y' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = chain 'Z' } ncs_group { reference = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 24.560 Check model and map are aligned: 0.480 Set scattering table: 0.250 Process input model: 87.900 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.220 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 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 : 0.009 0.062 31089 Z= 0.596 Angle : 1.367 10.937 43433 Z= 0.960 Chirality : 0.095 0.513 5065 Planarity : 0.006 0.054 4372 Dihedral : 23.547 179.930 13894 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 8.81 % Allowed : 12.27 % Favored : 78.91 % Cbeta Deviations : 0.66 % 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: -2.08 (0.14), residues: 2876 helix: -0.84 (0.11), residues: 1716 sheet: -1.86 (0.36), residues: 218 loop : -2.04 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP R 45 HIS 0.004 0.001 HIS S 43 PHE 0.017 0.002 PHE U 196 TYR 0.012 0.002 TYR X 275 ARG 0.026 0.001 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 341 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 63 ARG cc_start: 0.4484 (OUTLIER) cc_final: 0.3920 (ttm170) REVERT: R 91 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.6775 (p) REVERT: R 95 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8014 (tmm-80) REVERT: R 153 THR cc_start: 0.6204 (OUTLIER) cc_final: 0.5972 (p) REVERT: R 208 VAL cc_start: 0.8913 (t) cc_final: 0.8648 (t) REVERT: S 37 GLN cc_start: 0.9245 (tp40) cc_final: 0.8747 (pp30) REVERT: S 124 ASP cc_start: 0.9083 (m-30) cc_final: 0.8834 (t70) REVERT: S 130 ILE cc_start: 0.9049 (mt) cc_final: 0.8286 (mt) REVERT: S 159 ASP cc_start: 0.9182 (m-30) cc_final: 0.8914 (m-30) REVERT: S 255 SER cc_start: 0.3167 (OUTLIER) cc_final: 0.2158 (p) REVERT: S 264 ASP cc_start: 0.8684 (t70) cc_final: 0.8448 (m-30) REVERT: S 276 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5789 (mmtt) REVERT: T 156 ASP cc_start: 0.8562 (m-30) cc_final: 0.8003 (p0) REVERT: T 232 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5728 (mt) REVERT: T 255 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8051 (p) REVERT: U 91 VAL cc_start: 0.5209 (OUTLIER) cc_final: 0.4940 (p) REVERT: U 104 ASP cc_start: 0.9027 (m-30) cc_final: 0.8582 (t0) REVERT: U 117 VAL cc_start: 0.8658 (m) cc_final: 0.8120 (m) REVERT: V 95 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7174 (tmm-80) REVERT: V 213 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8956 (mp10) REVERT: W 159 ASP cc_start: 0.9052 (m-30) cc_final: 0.8668 (m-30) REVERT: W 271 VAL cc_start: 0.8419 (m) cc_final: 0.7996 (t) REVERT: X 36 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8064 (pp) REVERT: X 91 VAL cc_start: 0.4813 (OUTLIER) cc_final: 0.4509 (p) REVERT: X 108 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9135 (ptpp) REVERT: X 153 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6194 (p) REVERT: X 180 ILE cc_start: 0.6382 (pt) cc_final: 0.5996 (pt) REVERT: Y 95 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7114 (ptt90) REVERT: Y 199 LEU cc_start: -0.1685 (OUTLIER) cc_final: -0.2005 (mt) REVERT: Y 232 ILE cc_start: -0.0744 (OUTLIER) cc_final: -0.1020 (mm) REVERT: Y 255 SER cc_start: 0.5871 (OUTLIER) cc_final: 0.5356 (p) REVERT: Z 21 LEU cc_start: 0.7019 (tt) cc_final: 0.6751 (mt) REVERT: Z 36 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (pt) REVERT: Z 63 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8195 (ttp-170) REVERT: Z 81 GLN cc_start: 0.1313 (OUTLIER) cc_final: 0.0658 (pt0) REVERT: Z 113 LEU cc_start: 0.4936 (mt) cc_final: 0.4093 (mt) REVERT: Z 229 MET cc_start: -0.0517 (mmt) cc_final: -0.0753 (ttt) REVERT: Z 263 ILE cc_start: 0.0630 (OUTLIER) cc_final: 0.0320 (pt) outliers start: 214 outliers final: 37 residues processed: 536 average time/residue: 0.5652 time to fit residues: 431.4025 Evaluate side-chains 245 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 186 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 370 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS R 38 GLN S 38 GLN S 43 HIS T 38 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN V 38 GLN V 43 HIS W 38 GLN X 38 GLN ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN Y 43 HIS Z 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31089 Z= 0.252 Angle : 0.686 9.269 43433 Z= 0.364 Chirality : 0.042 0.441 5065 Planarity : 0.005 0.057 4372 Dihedral : 23.450 179.302 8056 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2876 helix: 0.31 (0.12), residues: 1750 sheet: -1.24 (0.46), residues: 153 loop : -1.80 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 211 HIS 0.010 0.001 HIS A 522 PHE 0.017 0.002 PHE A 305 TYR 0.036 0.002 TYR A 497 ARG 0.012 0.001 ARG U 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.2599 (ptm) cc_final: 0.1985 (ppp) REVERT: R 210 MET cc_start: 0.8762 (mmp) cc_final: 0.8522 (mmm) REVERT: R 214 MET cc_start: 0.9028 (tpp) cc_final: 0.8570 (tmm) REVERT: S 124 ASP cc_start: 0.9058 (m-30) cc_final: 0.8801 (t70) REVERT: S 159 ASP cc_start: 0.9232 (m-30) cc_final: 0.9008 (m-30) REVERT: S 264 ASP cc_start: 0.8254 (t70) cc_final: 0.7992 (p0) REVERT: T 19 GLU cc_start: 0.9658 (tm-30) cc_final: 0.9260 (pm20) REVERT: T 105 LEU cc_start: 0.8650 (mt) cc_final: 0.8435 (mp) REVERT: T 210 MET cc_start: 0.3263 (ttp) cc_final: 0.2957 (tmm) REVERT: U 104 ASP cc_start: 0.8971 (m-30) cc_final: 0.8770 (t0) REVERT: V 190 PHE cc_start: 0.8576 (m-10) cc_final: 0.8353 (m-80) REVERT: W 159 ASP cc_start: 0.8886 (m-30) cc_final: 0.8067 (m-30) REVERT: W 271 VAL cc_start: 0.7906 (m) cc_final: 0.7422 (m) REVERT: X 214 MET cc_start: 0.9148 (tpt) cc_final: 0.8825 (ttt) REVERT: Y 106 PHE cc_start: 0.8171 (m-80) cc_final: 0.7964 (m-80) REVERT: Y 159 ASP cc_start: 0.9492 (t0) cc_final: 0.9286 (t0) REVERT: Z 21 LEU cc_start: 0.7348 (tt) cc_final: 0.7106 (mt) REVERT: Z 229 MET cc_start: -0.1291 (mmt) cc_final: -0.1530 (ttm) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.5427 time to fit residues: 176.6743 Evaluate side-chains 141 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 290 optimal weight: 50.0000 chunk 313 optimal weight: 0.9980 chunk 258 optimal weight: 30.0000 chunk 287 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 494 GLN A 506 GLN R 81 GLN ** T 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 97 HIS ** W 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 GLN ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Z 185 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31089 Z= 0.208 Angle : 0.620 11.168 43433 Z= 0.330 Chirality : 0.040 0.340 5065 Planarity : 0.005 0.054 4372 Dihedral : 23.120 179.595 8056 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2876 helix: 0.64 (0.12), residues: 1741 sheet: -1.44 (0.42), residues: 155 loop : -1.49 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 211 HIS 0.008 0.001 HIS A 522 PHE 0.020 0.002 PHE Y 196 TYR 0.037 0.002 TYR Z 75 ARG 0.007 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.2462 (ptm) cc_final: 0.2191 (ppp) REVERT: A 357 LEU cc_start: 0.9569 (mt) cc_final: 0.9345 (pp) REVERT: R 210 MET cc_start: 0.8778 (mmp) cc_final: 0.8561 (mmp) REVERT: R 214 MET cc_start: 0.9184 (tpp) cc_final: 0.8780 (tmm) REVERT: S 124 ASP cc_start: 0.9054 (m-30) cc_final: 0.8824 (t70) REVERT: T 19 GLU cc_start: 0.9666 (tm-30) cc_final: 0.9278 (pm20) REVERT: U 104 ASP cc_start: 0.8992 (m-30) cc_final: 0.8547 (t0) REVERT: V 106 PHE cc_start: 0.8618 (m-80) cc_final: 0.8327 (m-80) REVERT: V 126 ARG cc_start: 0.9311 (ptm-80) cc_final: 0.9083 (tmm-80) REVERT: V 127 ASP cc_start: 0.9740 (m-30) cc_final: 0.9375 (m-30) REVERT: V 215 VAL cc_start: 0.7927 (t) cc_final: 0.7649 (t) REVERT: X 214 MET cc_start: 0.9270 (tpt) cc_final: 0.8991 (ttt) REVERT: Y 106 PHE cc_start: 0.8169 (m-80) cc_final: 0.7942 (m-80) REVERT: Z 21 LEU cc_start: 0.7456 (tt) cc_final: 0.7203 (mt) REVERT: Z 229 MET cc_start: -0.1136 (mmt) cc_final: -0.1376 (ttm) outliers start: 6 outliers final: 1 residues processed: 180 average time/residue: 0.5204 time to fit residues: 140.3296 Evaluate side-chains 119 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 64 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 469 ASN A 494 GLN A 556 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** S 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 GLN ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31089 Z= 0.315 Angle : 0.752 12.885 43433 Z= 0.401 Chirality : 0.044 0.300 5065 Planarity : 0.006 0.067 4372 Dihedral : 23.480 178.017 8056 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 0.21 % Allowed : 4.53 % Favored : 95.26 % 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: -1.02 (0.15), residues: 2876 helix: -0.03 (0.12), residues: 1745 sheet: -1.39 (0.35), residues: 218 loop : -1.54 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 20 HIS 0.010 0.002 HIS A 522 PHE 0.030 0.003 PHE T 125 TYR 0.023 0.003 TYR V 112 ARG 0.009 0.001 ARG Z 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3084 (ptm) cc_final: 0.2683 (ppp) REVERT: A 357 LEU cc_start: 0.9578 (mt) cc_final: 0.9369 (pp) REVERT: S 124 ASP cc_start: 0.9139 (m-30) cc_final: 0.8904 (t70) REVERT: T 19 GLU cc_start: 0.9692 (tm-30) cc_final: 0.9309 (pm20) REVERT: T 139 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8398 (tt0) REVERT: W 140 MET cc_start: 0.8511 (tpp) cc_final: 0.8162 (tpp) REVERT: X 190 PHE cc_start: 0.8300 (m-80) cc_final: 0.7931 (m-80) REVERT: X 214 MET cc_start: 0.9334 (tpt) cc_final: 0.9048 (ttt) REVERT: Z 21 LEU cc_start: 0.7660 (tt) cc_final: 0.7416 (mt) outliers start: 5 outliers final: 2 residues processed: 148 average time/residue: 0.4920 time to fit residues: 112.3221 Evaluate side-chains 99 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 229 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 263 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 77 optimal weight: 40.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 85 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 494 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31089 Z= 0.207 Angle : 0.615 8.330 43433 Z= 0.327 Chirality : 0.040 0.301 5065 Planarity : 0.005 0.050 4372 Dihedral : 23.238 179.544 8056 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2876 helix: 0.31 (0.12), residues: 1730 sheet: -1.61 (0.31), residues: 295 loop : -1.28 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP X 45 HIS 0.006 0.001 HIS A 522 PHE 0.021 0.002 PHE A 401 TYR 0.026 0.002 TYR Z 75 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.2793 (ptm) cc_final: 0.2476 (ppp) REVERT: A 291 MET cc_start: 0.7819 (mmp) cc_final: 0.5401 (tpp) REVERT: A 357 LEU cc_start: 0.9601 (mt) cc_final: 0.9395 (pp) REVERT: R 140 MET cc_start: 0.9259 (ppp) cc_final: 0.8843 (ppp) REVERT: R 210 MET cc_start: 0.8795 (mmp) cc_final: 0.8588 (mmp) REVERT: S 124 ASP cc_start: 0.9121 (m-30) cc_final: 0.8720 (t70) REVERT: T 19 GLU cc_start: 0.9703 (tm-30) cc_final: 0.9339 (pm20) REVERT: T 139 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8563 (tt0) REVERT: V 126 ARG cc_start: 0.9337 (ptm160) cc_final: 0.8936 (tmm-80) REVERT: V 127 ASP cc_start: 0.9728 (m-30) cc_final: 0.9337 (m-30) REVERT: V 215 VAL cc_start: 0.8496 (t) cc_final: 0.8169 (t) REVERT: W 140 MET cc_start: 0.8560 (tpp) cc_final: 0.8259 (tpp) REVERT: X 190 PHE cc_start: 0.8280 (m-80) cc_final: 0.7980 (m-80) REVERT: X 214 MET cc_start: 0.9365 (tpt) cc_final: 0.9086 (ttt) REVERT: Z 21 LEU cc_start: 0.7770 (tt) cc_final: 0.7501 (mt) REVERT: Z 75 TYR cc_start: 0.9005 (m-80) cc_final: 0.8800 (m-80) REVERT: Z 229 MET cc_start: -0.0033 (mmt) cc_final: -0.0272 (tpp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.4821 time to fit residues: 109.5704 Evaluate side-chains 108 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 308 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 496 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN S 37 GLN ** S 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** V 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 GLN Z 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.9439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 31089 Z= 0.390 Angle : 0.860 12.413 43433 Z= 0.455 Chirality : 0.048 0.404 5065 Planarity : 0.007 0.066 4372 Dihedral : 23.861 178.738 8056 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 39.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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 (0.14), residues: 2876 helix: -0.66 (0.11), residues: 1713 sheet: -2.18 (0.30), residues: 270 loop : -1.70 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP T 211 HIS 0.011 0.002 HIS A 500 PHE 0.043 0.004 PHE V 196 TYR 0.026 0.003 TYR S 73 ARG 0.009 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.9211 (ppp) cc_final: 0.8833 (ppp) REVERT: R 210 MET cc_start: 0.8785 (mmp) cc_final: 0.8562 (mmp) REVERT: S 124 ASP cc_start: 0.9088 (m-30) cc_final: 0.8831 (t70) REVERT: S 229 MET cc_start: -0.5016 (mtm) cc_final: -0.5332 (mmt) REVERT: T 139 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8563 (tt0) REVERT: V 126 ARG cc_start: 0.9426 (ptm160) cc_final: 0.8980 (tmm-80) REVERT: V 127 ASP cc_start: 0.9754 (m-30) cc_final: 0.9436 (m-30) REVERT: W 140 MET cc_start: 0.8555 (tpp) cc_final: 0.8188 (tpp) REVERT: X 97 HIS cc_start: 0.8238 (p90) cc_final: 0.7992 (p90) REVERT: Y 140 MET cc_start: 0.3672 (tpp) cc_final: 0.3334 (tpp) REVERT: Z 21 LEU cc_start: 0.8004 (tt) cc_final: 0.7750 (mt) REVERT: Z 75 TYR cc_start: 0.8931 (m-80) cc_final: 0.8717 (m-80) REVERT: Z 229 MET cc_start: 0.0775 (mmt) cc_final: 0.0014 (ttt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.5049 time to fit residues: 104.3997 Evaluate side-chains 96 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 307 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 496 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 GLN ** S 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.9425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31089 Z= 0.215 Angle : 0.665 9.600 43433 Z= 0.350 Chirality : 0.042 0.386 5065 Planarity : 0.005 0.051 4372 Dihedral : 23.482 177.439 8056 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2876 helix: -0.14 (0.12), residues: 1715 sheet: -1.95 (0.29), residues: 279 loop : -1.56 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 211 HIS 0.006 0.001 HIS S 97 PHE 0.020 0.002 PHE U 106 TYR 0.026 0.002 TYR A 497 ARG 0.007 0.001 ARG W 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3765 (ppp) cc_final: 0.3544 (ppp) REVERT: R 140 MET cc_start: 0.9259 (ppp) cc_final: 0.8868 (ppp) REVERT: R 210 MET cc_start: 0.8722 (mmp) cc_final: 0.8497 (mmp) REVERT: S 124 ASP cc_start: 0.9085 (m-30) cc_final: 0.8816 (t70) REVERT: S 229 MET cc_start: -0.4957 (mtm) cc_final: -0.5276 (mmt) REVERT: T 139 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8525 (tt0) REVERT: W 140 MET cc_start: 0.8536 (tpp) cc_final: 0.8148 (tpp) REVERT: W 210 MET cc_start: 0.8989 (ppp) cc_final: 0.8779 (ppp) REVERT: W 214 MET cc_start: 0.8423 (ptp) cc_final: 0.8200 (ptp) REVERT: Y 106 PHE cc_start: 0.8316 (m-80) cc_final: 0.8039 (m-80) REVERT: Y 140 MET cc_start: 0.4062 (tpp) cc_final: 0.3565 (tpp) REVERT: Z 21 LEU cc_start: 0.8010 (tt) cc_final: 0.7740 (mt) REVERT: Z 75 TYR cc_start: 0.8931 (m-80) cc_final: 0.8693 (m-80) REVERT: Z 229 MET cc_start: 0.0114 (mmt) cc_final: -0.0480 (ttm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.4561 time to fit residues: 98.9388 Evaluate side-chains 98 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 195 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 28 optimal weight: 0.0970 chunk 241 optimal weight: 50.0000 overall best weight: 2.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 GLN S 98 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.9403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31089 Z= 0.166 Angle : 0.600 9.471 43433 Z= 0.316 Chirality : 0.039 0.322 5065 Planarity : 0.004 0.050 4372 Dihedral : 23.048 179.341 8056 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2876 helix: 0.32 (0.12), residues: 1719 sheet: -1.83 (0.30), residues: 280 loop : -1.39 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 45 HIS 0.023 0.001 HIS X 43 PHE 0.016 0.001 PHE U 196 TYR 0.019 0.002 TYR A 80 ARG 0.006 0.001 ARG W 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3343 (ppp) cc_final: 0.2939 (ppp) REVERT: A 405 MET cc_start: -0.0826 (mtt) cc_final: -0.1132 (mtp) REVERT: R 140 MET cc_start: 0.9235 (ppp) cc_final: 0.8839 (ppp) REVERT: R 210 MET cc_start: 0.8727 (mmp) cc_final: 0.8492 (mmp) REVERT: S 124 ASP cc_start: 0.9081 (m-30) cc_final: 0.8803 (t70) REVERT: S 229 MET cc_start: -0.4985 (mtm) cc_final: -0.5317 (mmt) REVERT: T 139 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8565 (tt0) REVERT: V 126 ARG cc_start: 0.9482 (ptm-80) cc_final: 0.9098 (tmm-80) REVERT: V 127 ASP cc_start: 0.9704 (m-30) cc_final: 0.9222 (p0) REVERT: W 140 MET cc_start: 0.8582 (tpp) cc_final: 0.8260 (tpp) REVERT: Y 106 PHE cc_start: 0.8221 (m-80) cc_final: 0.7919 (m-80) REVERT: Y 140 MET cc_start: 0.4065 (tpp) cc_final: 0.3425 (tpp) REVERT: Z 21 LEU cc_start: 0.7944 (tt) cc_final: 0.7657 (mt) REVERT: Z 229 MET cc_start: -0.0059 (mmt) cc_final: -0.0658 (ttt) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.4546 time to fit residues: 105.2356 Evaluate side-chains 102 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 286 optimal weight: 30.0000 chunk 172 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 224 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 1.0178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31089 Z= 0.266 Angle : 0.699 10.673 43433 Z= 0.368 Chirality : 0.042 0.364 5065 Planarity : 0.005 0.052 4372 Dihedral : 23.262 179.299 8056 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -1.14 (0.15), residues: 2876 helix: -0.04 (0.12), residues: 1716 sheet: -1.89 (0.30), residues: 279 loop : -1.57 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 45 HIS 0.026 0.002 HIS X 43 PHE 0.024 0.002 PHE U 196 TYR 0.023 0.002 TYR A 497 ARG 0.016 0.001 ARG Z 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3599 (ppp) cc_final: 0.3256 (ppp) REVERT: A 291 MET cc_start: 0.8295 (mmp) cc_final: 0.7848 (mmp) REVERT: R 140 MET cc_start: 0.9213 (ppp) cc_final: 0.8840 (ppp) REVERT: S 124 ASP cc_start: 0.9090 (m-30) cc_final: 0.8826 (t70) REVERT: S 229 MET cc_start: -0.5008 (mtm) cc_final: -0.5340 (mmt) REVERT: T 276 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7807 (mmtm) REVERT: W 140 MET cc_start: 0.8501 (tpp) cc_final: 0.8158 (tpp) REVERT: X 97 HIS cc_start: 0.8227 (p90) cc_final: 0.7970 (p90) REVERT: X 193 HIS cc_start: 0.8525 (p90) cc_final: 0.8311 (p90) REVERT: Y 140 MET cc_start: 0.3799 (tpp) cc_final: 0.3367 (tpp) REVERT: Z 21 LEU cc_start: 0.8040 (tt) cc_final: 0.7764 (mt) REVERT: Z 140 MET cc_start: 0.6097 (ptp) cc_final: 0.5871 (ptp) REVERT: Z 229 MET cc_start: 0.0041 (mmt) cc_final: -0.0542 (ttt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4758 time to fit residues: 104.1349 Evaluate side-chains 106 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 184 optimal weight: 0.3980 chunk 143 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 HIS S 37 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 1.0415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31089 Z= 0.209 Angle : 0.639 9.865 43433 Z= 0.338 Chirality : 0.041 0.338 5065 Planarity : 0.005 0.054 4372 Dihedral : 23.134 178.787 8056 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 2876 helix: 0.08 (0.12), residues: 1716 sheet: -1.88 (0.30), residues: 280 loop : -1.56 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 211 HIS 0.023 0.001 HIS X 43 PHE 0.035 0.002 PHE Y 196 TYR 0.021 0.002 TYR A 497 ARG 0.011 0.001 ARG S 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3712 (ppp) cc_final: 0.3375 (ppp) REVERT: R 140 MET cc_start: 0.9207 (ppp) cc_final: 0.8829 (ppp) REVERT: S 124 ASP cc_start: 0.9091 (m-30) cc_final: 0.8828 (t70) REVERT: S 229 MET cc_start: -0.4985 (mtm) cc_final: -0.5304 (mmt) REVERT: T 139 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8564 (tt0) REVERT: W 140 MET cc_start: 0.8510 (tpp) cc_final: 0.8145 (tpp) REVERT: X 97 HIS cc_start: 0.8153 (p90) cc_final: 0.7876 (p90) REVERT: Y 140 MET cc_start: 0.4038 (tpp) cc_final: 0.3439 (tpp) REVERT: Z 140 MET cc_start: 0.6466 (ptp) cc_final: 0.6252 (ptp) REVERT: Z 229 MET cc_start: -0.0077 (mmt) cc_final: -0.0608 (ttm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.4775 time to fit residues: 104.9356 Evaluate side-chains 100 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 233 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 50.0000 chunk 253 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 GLN ** T 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.070954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.054200 restraints weight = 354675.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.054832 restraints weight = 314273.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.055310 restraints weight = 279675.260| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 1.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31089 Z= 0.181 Angle : 0.627 11.410 43433 Z= 0.330 Chirality : 0.040 0.343 5065 Planarity : 0.004 0.055 4372 Dihedral : 22.936 179.313 8056 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2876 helix: 0.29 (0.12), residues: 1715 sheet: -1.84 (0.30), residues: 280 loop : -1.50 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 45 HIS 0.022 0.001 HIS X 43 PHE 0.038 0.002 PHE Y 196 TYR 0.021 0.002 TYR A 497 ARG 0.007 0.001 ARG Y 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6044.14 seconds wall clock time: 112 minutes 22.93 seconds (6742.93 seconds total)