Starting phenix.real_space_refine on Mon Nov 18 07:09:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/11_2024/8sik_40508.cif" } resolution = 2.9 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= 0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 80 5.16 5 C 10196 2.51 5 N 2708 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15832 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "E" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.46 residue: pdb="CA CA F 201 " occ=0.45 residue: pdb="CA CA H 201 " occ=0.51 residue: pdb="CA CA H 203 " occ=0.49 Time building chain proxies: 10.23, per 1000 atoms: 0.65 Number of scatterers: 15832 At special positions: 0 Unit cell: (113.265, 113.265, 124.172, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 80 16.00 O 2840 8.00 N 2708 7.00 C 10196 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 - 3.00 Amino acid : True - 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: 4.28 Conformation dependent library (CDL) restraints added in 2.7 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 4 sheets defined 81.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.604A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.745A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.783A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.539A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.720A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.179A pdb=" N ILE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.527A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.607A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 358 removed outlier: 3.863A pdb=" N ILE A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.862A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 395 " --> pdb=" O TRP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 4.024A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 568 removed outlier: 3.585A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.560A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 139 through 149 removed outlier: 3.525A pdb=" N VAL D 143 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 149 " --> pdb=" O MET D 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.571A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.589A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.564A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.616A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.839A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 145 removed outlier: 3.830A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 178 removed outlier: 3.541A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.646A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.338A pdb=" N ILE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 242 removed outlier: 3.562A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP G 242 " --> pdb=" O LEU G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 242' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.609A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 358 removed outlier: 3.838A pdb=" N ILE G 337 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 389 through 396 removed outlier: 3.911A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR G 395 " --> pdb=" O TRP G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 4.185A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 519 " --> pdb=" O LYS G 515 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 568 removed outlier: 3.572A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.702A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 178 removed outlier: 3.593A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.654A pdb=" N GLY C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.236A pdb=" N ILE C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 removed outlier: 3.593A pdb=" N ASP C 242 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.604A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 358 removed outlier: 3.891A pdb=" N ILE C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 389 through 396 removed outlier: 3.876A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 395 " --> pdb=" O TRP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 4.337A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 568 removed outlier: 3.587A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 145 removed outlier: 3.804A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 178 removed outlier: 3.708A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.626A pdb=" N GLY E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.242A pdb=" N ILE E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.571A pdb=" N ASP E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.630A pdb=" N VAL E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 358 removed outlier: 3.877A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER E 338 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Proline residue: E 343 - end of helix Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 363 through 366 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 389 through 396 removed outlier: 3.856A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR E 395 " --> pdb=" O TRP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 4.267A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 567 removed outlier: 3.581A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1112 hydrogen bonds defined for protein. 3306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5098 1.34 - 1.46: 2385 1.46 - 1.57: 8533 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 16152 Sorted by residual: bond pdb=" C ILE A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" C ILE C 368 " pdb=" N PRO C 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.05e+00 bond pdb=" C GLY D 26 " pdb=" O GLY D 26 " ideal model delta sigma weight residual 1.239 1.222 0.017 1.09e-02 8.42e+03 2.44e+00 bond pdb=" CA LYS D 22 " pdb=" C LYS D 22 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.85e+00 bond pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " ideal model delta sigma weight residual 1.530 1.550 -0.020 2.00e-02 2.50e+03 1.00e+00 ... (remaining 16147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 21507 1.74 - 3.47: 271 3.47 - 5.21: 35 5.21 - 6.94: 7 6.94 - 8.68: 4 Bond angle restraints: 21824 Sorted by residual: angle pdb=" N ILE A 227 " pdb=" CA ILE A 227 " pdb=" C ILE A 227 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CD1 ILE B 131 " ideal model delta sigma weight residual 113.80 120.89 -7.09 2.10e+00 2.27e-01 1.14e+01 angle pdb=" N GLY D 26 " pdb=" CA GLY D 26 " pdb=" C GLY D 26 " ideal model delta sigma weight residual 114.95 110.49 4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" CG ARG E 507 " pdb=" CD ARG E 507 " pdb=" NE ARG E 507 " ideal model delta sigma weight residual 112.00 118.29 -6.29 2.20e+00 2.07e-01 8.17e+00 angle pdb=" CA GLU D 12 " pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.04e+00 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8299 17.48 - 34.96: 897 34.96 - 52.44: 251 52.44 - 69.93: 20 69.93 - 87.41: 25 Dihedral angle restraints: 9492 sinusoidal: 3776 harmonic: 5716 Sorted by residual: dihedral pdb=" CA GLN E 234 " pdb=" C GLN E 234 " pdb=" N ILE E 235 " pdb=" CA ILE E 235 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CG ARG G 109 " pdb=" CD ARG G 109 " pdb=" NE ARG G 109 " pdb=" CZ ARG G 109 " ideal model delta sinusoidal sigma weight residual 90.00 134.49 -44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 170 " pdb=" CG GLU A 170 " pdb=" CD GLU A 170 " pdb=" OE1 GLU A 170 " ideal model delta sinusoidal sigma weight residual 0.00 -86.93 86.93 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1972 0.049 - 0.097: 406 0.097 - 0.146: 60 0.146 - 0.194: 1 0.194 - 0.243: 5 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CG LEU G 191 " pdb=" CB LEU G 191 " pdb=" CD1 LEU G 191 " pdb=" CD2 LEU G 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ASN F 43 " pdb=" N ASN F 43 " pdb=" C ASN F 43 " pdb=" CB ASN F 43 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU E 191 " pdb=" CB LEU E 191 " pdb=" CD1 LEU E 191 " pdb=" CD2 LEU E 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2441 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ASP D 21 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 22 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 507 " 0.196 9.50e-02 1.11e+02 8.81e-02 5.33e+00 pdb=" NE ARG G 507 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 507 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 507 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 507 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 131 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C ILE B 131 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 131 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 132 " 0.008 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1625 2.74 - 3.28: 16120 3.28 - 3.82: 26892 3.82 - 4.36: 31323 4.36 - 4.90: 55056 Nonbonded interactions: 131016 Sorted by model distance: nonbonded pdb=" OE2 GLU H 68 " pdb="CA CA H 203 " model vdw 2.206 2.510 nonbonded pdb=" OE1 GLU H 55 " pdb=" NZ LYS G 527 " model vdw 2.209 3.120 nonbonded pdb=" OD1 ASN H 61 " pdb="CA CA H 203 " model vdw 2.211 2.510 nonbonded pdb=" OE1 GLU H 124 " pdb=" OG SER G 390 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU B 124 " pdb=" OG SER A 390 " model vdw 2.268 3.040 ... (remaining 131011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 6 through 149 or resid 201)) selection = (chain 'D' and (resid 6 through 149 or resid 201)) selection = chain 'F' selection = (chain 'H' and (resid 6 through 149 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.790 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.003 0.026 16152 Z= 0.181 Angle : 0.506 8.678 21824 Z= 0.296 Chirality : 0.039 0.243 2444 Planarity : 0.004 0.088 2752 Dihedral : 15.666 87.408 5812 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.96 % Allowed : 19.64 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.12 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 323 HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE E 332 TYR 0.017 0.001 TYR D 139 ARG 0.013 0.001 ARG G 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 1.736 Fit side-chains REVERT: G 195 ARG cc_start: 0.6353 (mtp180) cc_final: 0.5956 (mtm110) REVERT: C 191 LEU cc_start: 0.6722 (mp) cc_final: 0.6407 (mm) outliers start: 16 outliers final: 12 residues processed: 216 average time/residue: 1.5645 time to fit residues: 369.1115 Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16152 Z= 0.236 Angle : 0.476 7.676 21824 Z= 0.263 Chirality : 0.039 0.214 2444 Planarity : 0.004 0.046 2752 Dihedral : 4.000 37.967 2182 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.43 % Allowed : 16.57 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1952 helix: 2.12 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 323 HIS 0.003 0.001 HIS C 240 PHE 0.014 0.001 PHE C 332 TYR 0.013 0.002 TYR C 545 ARG 0.006 0.000 ARG G 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.853 Fit side-chains REVERT: B 131 ILE cc_start: 0.4312 (OUTLIER) cc_final: 0.4060 (pp) REVERT: A 191 LEU cc_start: 0.6220 (mp) cc_final: 0.5921 (mm) REVERT: D 112 ASN cc_start: 0.8615 (m-40) cc_final: 0.8380 (m-40) REVERT: F 42 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: F 68 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: F 140 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: H 112 ASN cc_start: 0.8603 (m-40) cc_final: 0.8379 (m-40) REVERT: H 141 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6653 (pp20) REVERT: G 195 ARG cc_start: 0.6406 (mtp180) cc_final: 0.5923 (mtm110) REVERT: C 191 LEU cc_start: 0.6267 (mp) cc_final: 0.5931 (mm) outliers start: 57 outliers final: 21 residues processed: 242 average time/residue: 1.5628 time to fit residues: 411.9274 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16152 Z= 0.163 Angle : 0.435 6.784 21824 Z= 0.239 Chirality : 0.037 0.229 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.450 23.649 2170 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.83 % Allowed : 17.05 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.19), residues: 1952 helix: 2.28 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 379 HIS 0.004 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.011 0.001 TYR C 545 ARG 0.006 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.872 Fit side-chains REVERT: A 557 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6486 (mtpt) REVERT: D 12 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: D 112 ASN cc_start: 0.8552 (m-40) cc_final: 0.8289 (m-40) REVERT: F 140 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: H 112 ASN cc_start: 0.8536 (m-40) cc_final: 0.8265 (m-40) REVERT: H 141 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6615 (pp20) REVERT: G 195 ARG cc_start: 0.6347 (mtp180) cc_final: 0.5852 (mtm110) REVERT: G 508 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: C 533 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7031 (mtm180) outliers start: 47 outliers final: 18 residues processed: 241 average time/residue: 1.5886 time to fit residues: 416.5682 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16152 Z= 0.150 Angle : 0.425 6.295 21824 Z= 0.233 Chirality : 0.037 0.239 2444 Planarity : 0.003 0.028 2752 Dihedral : 3.306 17.603 2168 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.89 % Allowed : 17.11 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.19), residues: 1952 helix: 2.26 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.26 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 323 HIS 0.003 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.011 0.001 TYR C 545 ARG 0.006 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 2.048 Fit side-chains REVERT: B 141 GLU cc_start: 0.7124 (pt0) cc_final: 0.6754 (pp20) REVERT: A 557 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6474 (mtpt) REVERT: D 12 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: D 112 ASN cc_start: 0.8542 (m-40) cc_final: 0.8287 (m-40) REVERT: F 42 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.6657 (mp10) REVERT: F 112 ASN cc_start: 0.8409 (m-40) cc_final: 0.7980 (m-40) REVERT: F 140 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: H 112 ASN cc_start: 0.8510 (m-40) cc_final: 0.8264 (m-40) REVERT: H 141 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6591 (pp20) REVERT: G 195 ARG cc_start: 0.6296 (mtp180) cc_final: 0.5807 (mtm110) REVERT: C 533 ARG cc_start: 0.7489 (mtp85) cc_final: 0.6973 (mtm180) REVERT: E 560 GLN cc_start: 0.6593 (tp-100) cc_final: 0.6054 (mt0) outliers start: 48 outliers final: 23 residues processed: 247 average time/residue: 1.5232 time to fit residues: 410.3003 Evaluate side-chains 236 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16152 Z= 0.200 Angle : 0.447 6.473 21824 Z= 0.245 Chirality : 0.038 0.259 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.367 17.494 2168 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.13 % Allowed : 16.93 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.19), residues: 1952 helix: 2.18 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 323 HIS 0.004 0.001 HIS G 363 PHE 0.013 0.001 PHE E 332 TYR 0.013 0.001 TYR C 545 ARG 0.004 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.778 Fit side-chains REVERT: B 141 GLU cc_start: 0.7228 (pt0) cc_final: 0.6906 (pp20) REVERT: A 557 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6526 (mtpt) REVERT: D 12 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: D 112 ASN cc_start: 0.8530 (m-40) cc_final: 0.8245 (m-40) REVERT: F 42 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: F 140 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: H 112 ASN cc_start: 0.8520 (m-40) cc_final: 0.8245 (m-40) REVERT: H 141 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: G 195 ARG cc_start: 0.6299 (mtp180) cc_final: 0.5792 (mtm110) REVERT: C 533 ARG cc_start: 0.7477 (mtp85) cc_final: 0.6761 (mtm110) REVERT: E 560 GLN cc_start: 0.6536 (tp-100) cc_final: 0.6022 (mt0) outliers start: 52 outliers final: 29 residues processed: 246 average time/residue: 1.5218 time to fit residues: 408.3234 Evaluate side-chains 239 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16152 Z= 0.166 Angle : 0.435 7.296 21824 Z= 0.237 Chirality : 0.037 0.254 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.323 17.661 2168 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.01 % Allowed : 17.47 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.19), residues: 1952 helix: 2.25 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 323 HIS 0.004 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.012 0.001 TYR C 545 ARG 0.002 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.816 Fit side-chains REVERT: B 141 GLU cc_start: 0.7218 (pt0) cc_final: 0.6886 (pp20) REVERT: A 557 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6510 (mtpt) REVERT: D 12 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: D 112 ASN cc_start: 0.8502 (m-40) cc_final: 0.8213 (m-40) REVERT: F 42 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: F 140 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: H 112 ASN cc_start: 0.8485 (m-40) cc_final: 0.8215 (m-40) REVERT: H 141 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6592 (pp20) REVERT: G 195 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5856 (mtm110) REVERT: C 533 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6703 (mtm110) outliers start: 50 outliers final: 26 residues processed: 247 average time/residue: 1.5226 time to fit residues: 410.1909 Evaluate side-chains 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN D 42 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16152 Z= 0.167 Angle : 0.443 7.999 21824 Z= 0.241 Chirality : 0.037 0.259 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.320 17.639 2168 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.31 % Allowed : 17.35 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.19), residues: 1952 helix: 2.25 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 323 HIS 0.005 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.012 0.001 TYR C 545 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 1.994 Fit side-chains REVERT: B 141 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 557 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6507 (mtpt) REVERT: D 12 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: D 112 ASN cc_start: 0.8504 (m-40) cc_final: 0.8221 (m-40) REVERT: F 39 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (p) REVERT: F 140 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: H 112 ASN cc_start: 0.8478 (m-40) cc_final: 0.8193 (m-40) REVERT: H 141 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: G 195 ARG cc_start: 0.6276 (mtp180) cc_final: 0.5860 (mtm110) REVERT: G 508 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5822 (mp0) REVERT: C 533 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6765 (mtm110) outliers start: 55 outliers final: 32 residues processed: 252 average time/residue: 1.5025 time to fit residues: 414.7936 Evaluate side-chains 251 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16152 Z= 0.184 Angle : 0.456 7.661 21824 Z= 0.248 Chirality : 0.037 0.259 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.351 17.591 2168 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.89 % Allowed : 17.35 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 1952 helix: 2.22 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 323 HIS 0.005 0.001 HIS G 363 PHE 0.012 0.001 PHE E 332 TYR 0.013 0.001 TYR C 545 ARG 0.003 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 1.994 Fit side-chains REVERT: B 141 GLU cc_start: 0.7217 (pt0) cc_final: 0.6889 (pp20) REVERT: A 557 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6506 (mtpt) REVERT: D 12 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: D 112 ASN cc_start: 0.8510 (m-40) cc_final: 0.8225 (m-40) REVERT: F 39 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8205 (p) REVERT: F 140 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: H 112 ASN cc_start: 0.8487 (m-40) cc_final: 0.8203 (m-40) REVERT: H 141 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6632 (pp20) REVERT: G 195 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5848 (mtm110) REVERT: G 508 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: C 533 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6782 (mtm110) REVERT: E 191 LEU cc_start: 0.6595 (mp) cc_final: 0.6258 (mm) outliers start: 48 outliers final: 32 residues processed: 244 average time/residue: 1.5724 time to fit residues: 417.1877 Evaluate side-chains 248 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16152 Z= 0.184 Angle : 0.461 8.211 21824 Z= 0.250 Chirality : 0.038 0.257 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.360 17.619 2168 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.59 % Allowed : 17.59 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 1952 helix: 2.22 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 323 HIS 0.006 0.001 HIS G 363 PHE 0.012 0.001 PHE G 332 TYR 0.012 0.001 TYR C 545 ARG 0.003 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.852 Fit side-chains REVERT: B 141 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6883 (pp20) REVERT: A 557 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6490 (mtpt) REVERT: D 12 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: D 112 ASN cc_start: 0.8505 (m-40) cc_final: 0.8216 (m-40) REVERT: F 39 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8205 (p) REVERT: F 140 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: H 112 ASN cc_start: 0.8492 (m-40) cc_final: 0.8214 (m-40) REVERT: H 141 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: G 191 LEU cc_start: 0.6660 (mm) cc_final: 0.6355 (mp) REVERT: G 195 ARG cc_start: 0.6261 (mtp180) cc_final: 0.5840 (mtm110) REVERT: G 508 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: C 533 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6778 (mtm110) REVERT: E 191 LEU cc_start: 0.6582 (mp) cc_final: 0.6246 (mm) outliers start: 43 outliers final: 32 residues processed: 238 average time/residue: 1.5232 time to fit residues: 396.2256 Evaluate side-chains 248 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 195 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16152 Z= 0.149 Angle : 0.449 8.039 21824 Z= 0.242 Chirality : 0.037 0.245 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.288 17.704 2168 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 18.07 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.19), residues: 1952 helix: 2.30 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.006 0.001 HIS G 363 PHE 0.011 0.001 PHE E 332 TYR 0.010 0.001 TYR C 545 ARG 0.003 0.000 ARG A 562 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.665 Fit side-chains REVERT: B 141 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: A 557 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6502 (mtpt) REVERT: D 12 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: D 112 ASN cc_start: 0.8476 (m-40) cc_final: 0.8232 (m-40) REVERT: F 39 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8208 (p) REVERT: F 140 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: H 112 ASN cc_start: 0.8467 (m-40) cc_final: 0.8231 (m-40) REVERT: H 141 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: G 191 LEU cc_start: 0.6638 (mm) cc_final: 0.6341 (mp) REVERT: G 195 ARG cc_start: 0.6218 (mtp180) cc_final: 0.5806 (mtm110) REVERT: C 533 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6693 (mtm110) REVERT: E 191 LEU cc_start: 0.6518 (mp) cc_final: 0.6179 (mm) outliers start: 35 outliers final: 28 residues processed: 237 average time/residue: 1.5207 time to fit residues: 394.5593 Evaluate side-chains 243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147213 restraints weight = 15689.979| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.89 r_work: 0.3448 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16152 Z= 0.285 Angle : 0.522 6.907 21824 Z= 0.284 Chirality : 0.040 0.241 2444 Planarity : 0.003 0.029 2752 Dihedral : 3.530 17.455 2168 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.41 % Allowed : 17.95 % Favored : 79.64 % 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: 2.29 (0.18), residues: 1952 helix: 1.99 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.27 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 323 HIS 0.008 0.001 HIS G 363 PHE 0.015 0.001 PHE C 332 TYR 0.017 0.002 TYR H 139 ARG 0.003 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6318.31 seconds wall clock time: 113 minutes 43.28 seconds (6823.28 seconds total)