Starting phenix.real_space_refine on Sat Jan 20 06:20:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n28_9326/01_2024/6n28_9326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n28_9326/01_2024/6n28_9326.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/6n28_9326/01_2024/6n28_9326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n28_9326/01_2024/6n28_9326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n28_9326/01_2024/6n28_9326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n28_9326/01_2024/6n28_9326_neut.pdb" } 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= 0.001 sd= 0.010 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 5 9.91 5 S 65 5.16 5 C 9110 2.51 5 N 2255 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.81, per 1000 atoms: 0.56 Number of scatterers: 13885 At special positions: 0 Unit cell: (95.744, 96.832, 112.064, 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 5 19.99 S 65 16.00 O 2450 8.00 N 2255 7.00 C 9110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.5 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.722A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.722A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.593A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.807A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 removed outlier: 3.610A pdb=" N TYR C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.673A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.569A pdb=" N THR C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.807A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 84 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.859A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.722A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.593A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 53 Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.722A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.569A pdb=" N THR E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2505 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: 3.98 Time building geometry restraints manager: 5.84 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: 4296 1.34 - 1.46: 3762 1.46 - 1.59: 6112 1.59 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 14270 Sorted by residual: bond pdb=" CB VAL D 81 " pdb=" CG1 VAL D 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 bond pdb=" CB VAL C 81 " pdb=" CG1 VAL C 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 bond pdb=" CB VAL A 81 " pdb=" CG1 VAL A 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL B 81 " pdb=" CG1 VAL B 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL E 81 " pdb=" CG1 VAL E 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 14265 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.46: 352 106.46 - 113.35: 7570 113.35 - 120.24: 5783 120.24 - 127.14: 5557 127.14 - 134.03: 173 Bond angle restraints: 19435 Sorted by residual: angle pdb=" C LEU D 271 " pdb=" N PHE D 272 " pdb=" CA PHE D 272 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C LEU C 271 " pdb=" N PHE C 272 " pdb=" CA PHE C 272 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU A 271 " pdb=" N PHE A 272 " pdb=" CA PHE A 272 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU E 271 " pdb=" N PHE E 272 " pdb=" CA PHE E 272 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU B 271 " pdb=" N PHE B 272 " pdb=" CA PHE B 272 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 19430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 7950 14.93 - 29.86: 270 29.86 - 44.79: 90 44.79 - 59.72: 10 59.72 - 74.65: 10 Dihedral angle restraints: 8330 sinusoidal: 3310 harmonic: 5020 Sorted by residual: dihedral pdb=" CA PRO B 103 " pdb=" C PRO B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PRO A 103 " pdb=" C PRO A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO E 103 " pdb=" C PRO E 103 " pdb=" N ASP E 104 " pdb=" CA ASP E 104 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1296 0.041 - 0.082: 633 0.082 - 0.124: 176 0.124 - 0.165: 15 0.165 - 0.206: 30 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU E 258 " pdb=" CB LEU E 258 " pdb=" CD1 LEU E 258 " pdb=" CD2 LEU E 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2147 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 282 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C PHE C 282 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE C 282 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE C 283 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 282 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C PHE D 282 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE D 282 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE D 283 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 282 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C PHE A 282 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE A 282 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 283 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1731 2.75 - 3.29: 13096 3.29 - 3.83: 23531 3.83 - 4.36: 27752 4.36 - 4.90: 48778 Nonbonded interactions: 114888 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN A 296 " pdb="CA CA A 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN D 296 " pdb="CA CA D 401 " model vdw 2.216 2.510 ... (remaining 114883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 1.580 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 38.590 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.006 0.051 14270 Z= 0.388 Angle : 0.780 7.915 19435 Z= 0.432 Chirality : 0.052 0.206 2150 Planarity : 0.007 0.045 2430 Dihedral : 9.537 74.652 5075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -3.44 (0.15), residues: 1680 helix: -1.88 (0.11), residues: 1135 sheet: None (None), residues: 0 loop : -2.86 (0.21), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 94 HIS 0.009 0.003 HIS C 326 PHE 0.021 0.003 PHE E 283 TYR 0.011 0.002 TYR E 97 ARG 0.005 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.651 Fit side-chains REVERT: A 58 GLN cc_start: 0.8567 (mt0) cc_final: 0.8328 (mt0) REVERT: B 18 SER cc_start: 0.9041 (m) cc_final: 0.8768 (t) REVERT: B 58 GLN cc_start: 0.8517 (mt0) cc_final: 0.8308 (mt0) REVERT: B 129 MET cc_start: 0.9092 (mmm) cc_final: 0.8888 (mmt) REVERT: B 320 MET cc_start: 0.8599 (ttt) cc_final: 0.8300 (ttm) REVERT: C 18 SER cc_start: 0.8999 (m) cc_final: 0.8625 (t) REVERT: C 175 ASN cc_start: 0.8385 (t0) cc_final: 0.8178 (t0) REVERT: C 249 LEU cc_start: 0.9206 (tp) cc_final: 0.8985 (mm) REVERT: D 249 LEU cc_start: 0.9264 (tp) cc_final: 0.9031 (mm) REVERT: D 334 LYS cc_start: 0.8731 (mttt) cc_final: 0.8459 (mttp) REVERT: E 18 SER cc_start: 0.9101 (m) cc_final: 0.8783 (t) REVERT: E 58 GLN cc_start: 0.8597 (mt0) cc_final: 0.8381 (mt0) REVERT: E 334 LYS cc_start: 0.8793 (mttt) cc_final: 0.8571 (mmtp) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 1.4084 time to fit residues: 414.9145 Evaluate side-chains 125 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 293 GLN B 19 GLN B 133 ASN D 58 GLN D 256 GLN E 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14270 Z= 0.222 Angle : 0.516 7.731 19435 Z= 0.269 Chirality : 0.039 0.157 2150 Planarity : 0.004 0.029 2430 Dihedral : 3.894 14.365 1875 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.65 % Allowed : 8.91 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1680 helix: 0.11 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 94 HIS 0.003 0.001 HIS C 326 PHE 0.013 0.002 PHE A 272 TYR 0.018 0.001 TYR D 97 ARG 0.005 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.795 Fit side-chains REVERT: A 61 MET cc_start: 0.7622 (tpt) cc_final: 0.7410 (tpt) REVERT: B 58 GLN cc_start: 0.8498 (mt0) cc_final: 0.8157 (mt0) REVERT: B 196 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8332 (tpt-90) REVERT: B 320 MET cc_start: 0.8805 (ttt) cc_final: 0.8566 (ttm) REVERT: D 61 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5947 (ttp) REVERT: E 18 SER cc_start: 0.9046 (m) cc_final: 0.8761 (t) REVERT: E 58 GLN cc_start: 0.8486 (mt0) cc_final: 0.8218 (mt0) REVERT: E 65 LEU cc_start: 0.8894 (tp) cc_final: 0.8536 (tp) REVERT: E 149 LYS cc_start: 0.8780 (mttm) cc_final: 0.8492 (mttm) REVERT: E 333 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7155 (mm-30) outliers start: 25 outliers final: 5 residues processed: 147 average time/residue: 1.2451 time to fit residues: 201.8493 Evaluate side-chains 111 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14270 Z= 0.192 Angle : 0.475 6.557 19435 Z= 0.248 Chirality : 0.038 0.156 2150 Planarity : 0.003 0.024 2430 Dihedral : 3.617 12.634 1875 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.11 % Allowed : 8.78 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1680 helix: 1.11 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -2.21 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 PHE 0.015 0.001 PHE A 272 TYR 0.018 0.001 TYR B 97 ARG 0.003 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.891 Fit side-chains REVERT: A 61 MET cc_start: 0.7681 (tpt) cc_final: 0.7394 (tpt) REVERT: B 196 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8311 (tpt-90) REVERT: B 320 MET cc_start: 0.8846 (ttt) cc_final: 0.8640 (ttm) REVERT: C 30 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8236 (ttmt) REVERT: C 61 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.6150 (ttp) REVERT: C 196 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8277 (tpt-90) REVERT: C 262 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8231 (mmtm) REVERT: D 61 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5887 (ttp) REVERT: E 18 SER cc_start: 0.8996 (m) cc_final: 0.8743 (t) REVERT: E 65 LEU cc_start: 0.8828 (tp) cc_final: 0.8442 (tp) REVERT: E 333 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 32 outliers final: 9 residues processed: 137 average time/residue: 1.2277 time to fit residues: 185.2470 Evaluate side-chains 111 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 159 optimal weight: 0.2980 chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14270 Z= 0.216 Angle : 0.474 5.399 19435 Z= 0.248 Chirality : 0.039 0.156 2150 Planarity : 0.003 0.025 2430 Dihedral : 3.547 12.579 1875 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.91 % Allowed : 9.50 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1680 helix: 1.51 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 94 HIS 0.003 0.001 HIS C 326 PHE 0.017 0.001 PHE A 272 TYR 0.019 0.001 TYR B 97 ARG 0.003 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.745 Fit side-chains REVERT: A 61 MET cc_start: 0.7704 (tpt) cc_final: 0.7371 (tpt) REVERT: B 196 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (tpt-90) REVERT: B 320 MET cc_start: 0.8911 (ttt) cc_final: 0.8687 (ttm) REVERT: C 196 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8307 (tpt-90) REVERT: C 262 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8258 (mmtm) REVERT: D 61 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5853 (ttp) REVERT: E 18 SER cc_start: 0.9011 (m) cc_final: 0.8775 (t) REVERT: E 65 LEU cc_start: 0.8792 (tp) cc_final: 0.8427 (tp) outliers start: 29 outliers final: 10 residues processed: 127 average time/residue: 1.2153 time to fit residues: 169.4401 Evaluate side-chains 111 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14270 Z= 0.154 Angle : 0.438 5.305 19435 Z= 0.231 Chirality : 0.037 0.155 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.415 11.802 1875 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.31 % Allowed : 10.30 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1680 helix: 1.75 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.002 0.000 HIS B 326 PHE 0.013 0.001 PHE A 272 TYR 0.015 0.001 TYR B 97 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.818 Fit side-chains REVERT: A 61 MET cc_start: 0.7712 (tpt) cc_final: 0.7419 (tpt) REVERT: B 320 MET cc_start: 0.8869 (ttt) cc_final: 0.8651 (ttm) REVERT: C 262 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8237 (mmtt) REVERT: D 18 SER cc_start: 0.8967 (m) cc_final: 0.8765 (t) REVERT: E 18 SER cc_start: 0.8948 (m) cc_final: 0.8725 (t) REVERT: E 65 LEU cc_start: 0.8827 (tp) cc_final: 0.8431 (tp) REVERT: E 333 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7023 (mm-30) outliers start: 35 outliers final: 11 residues processed: 131 average time/residue: 1.1997 time to fit residues: 174.8868 Evaluate side-chains 115 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 0.0770 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14270 Z= 0.221 Angle : 0.476 8.105 19435 Z= 0.247 Chirality : 0.039 0.156 2150 Planarity : 0.003 0.027 2430 Dihedral : 3.479 12.210 1875 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.71 % Allowed : 10.10 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1680 helix: 1.57 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.003 0.001 HIS C 326 PHE 0.017 0.001 PHE E 272 TYR 0.019 0.001 TYR B 97 ARG 0.002 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 1.821 Fit side-chains REVERT: B 196 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8360 (tpt-90) REVERT: B 320 MET cc_start: 0.8949 (ttt) cc_final: 0.8704 (ttm) REVERT: C 196 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8273 (tpt-90) REVERT: C 262 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8190 (mmtt) REVERT: D 18 SER cc_start: 0.8987 (m) cc_final: 0.8774 (t) REVERT: D 61 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5632 (ttp) REVERT: E 18 SER cc_start: 0.8996 (m) cc_final: 0.8779 (t) REVERT: E 65 LEU cc_start: 0.8795 (tp) cc_final: 0.8440 (tp) REVERT: E 333 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7066 (mm-30) outliers start: 41 outliers final: 18 residues processed: 130 average time/residue: 1.1972 time to fit residues: 171.8036 Evaluate side-chains 121 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14270 Z= 0.138 Angle : 0.439 7.275 19435 Z= 0.228 Chirality : 0.037 0.154 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.339 13.062 1875 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.05 % Allowed : 10.96 % Favored : 87.00 % 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: 1.38 (0.21), residues: 1680 helix: 1.90 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.71 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.000 HIS C 326 PHE 0.016 0.001 PHE E 272 TYR 0.014 0.001 TYR D 97 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.630 Fit side-chains REVERT: B 196 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8369 (tpt-90) REVERT: B 320 MET cc_start: 0.8874 (ttt) cc_final: 0.8651 (ttm) REVERT: C 196 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8287 (tpt-90) REVERT: C 262 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8175 (mmtt) REVERT: D 18 SER cc_start: 0.8939 (m) cc_final: 0.8720 (t) REVERT: E 18 SER cc_start: 0.8918 (m) cc_final: 0.8591 (t) REVERT: E 65 LEU cc_start: 0.8828 (tp) cc_final: 0.8446 (tp) REVERT: E 333 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7017 (mm-30) outliers start: 31 outliers final: 17 residues processed: 130 average time/residue: 1.1977 time to fit residues: 172.7672 Evaluate side-chains 117 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 144 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN E 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14270 Z= 0.154 Angle : 0.452 7.960 19435 Z= 0.232 Chirality : 0.037 0.154 2150 Planarity : 0.003 0.027 2430 Dihedral : 3.319 12.891 1875 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.11 % Allowed : 11.09 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1680 helix: 1.95 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 94 HIS 0.002 0.000 HIS C 326 PHE 0.018 0.001 PHE E 272 TYR 0.016 0.001 TYR B 97 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.707 Fit side-chains REVERT: B 196 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8375 (tpt-90) REVERT: B 320 MET cc_start: 0.8913 (ttt) cc_final: 0.8686 (ttm) REVERT: C 196 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8320 (tpt-90) REVERT: C 262 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8289 (mmtt) REVERT: D 18 SER cc_start: 0.8964 (m) cc_final: 0.8746 (t) REVERT: E 18 SER cc_start: 0.8922 (m) cc_final: 0.8713 (t) REVERT: E 65 LEU cc_start: 0.8788 (tp) cc_final: 0.8407 (tp) REVERT: E 333 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7055 (mm-30) outliers start: 32 outliers final: 19 residues processed: 130 average time/residue: 1.1919 time to fit residues: 171.9369 Evaluate side-chains 122 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 14270 Z= 0.442 Angle : 0.595 8.474 19435 Z= 0.303 Chirality : 0.044 0.158 2150 Planarity : 0.004 0.027 2430 Dihedral : 3.768 13.716 1875 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.78 % Allowed : 11.68 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1680 helix: 1.62 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 229 HIS 0.006 0.001 HIS C 326 PHE 0.025 0.002 PHE E 248 TYR 0.022 0.002 TYR B 97 ARG 0.005 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.757 Fit side-chains REVERT: B 196 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8364 (tpt-90) REVERT: B 320 MET cc_start: 0.9071 (ttt) cc_final: 0.8742 (ttm) REVERT: C 196 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8345 (tpt-90) REVERT: C 262 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8253 (mmtt) REVERT: E 65 LEU cc_start: 0.8817 (tp) cc_final: 0.8466 (tp) REVERT: E 333 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7196 (mm-30) outliers start: 27 outliers final: 10 residues processed: 117 average time/residue: 1.3700 time to fit residues: 175.8363 Evaluate side-chains 109 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 101 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14270 Z= 0.128 Angle : 0.460 7.855 19435 Z= 0.235 Chirality : 0.037 0.156 2150 Planarity : 0.003 0.029 2430 Dihedral : 3.409 12.439 1875 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 12.67 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1680 helix: 1.94 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.002 0.001 HIS B 168 PHE 0.021 0.001 PHE E 272 TYR 0.014 0.001 TYR E 97 ARG 0.003 0.000 ARG C 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.809 Fit side-chains REVERT: B 320 MET cc_start: 0.8834 (ttt) cc_final: 0.8577 (ttm) REVERT: C 262 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8267 (mmtt) REVERT: E 65 LEU cc_start: 0.8826 (tp) cc_final: 0.8432 (tp) outliers start: 16 outliers final: 9 residues processed: 115 average time/residue: 1.3007 time to fit residues: 164.9365 Evaluate side-chains 105 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 0.0060 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.072474 restraints weight = 21706.406| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.07 r_work: 0.2682 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14270 Z= 0.181 Angle : 0.482 7.857 19435 Z= 0.244 Chirality : 0.038 0.155 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.387 12.690 1875 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.92 % Allowed : 12.94 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1680 helix: 1.91 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.003 0.001 HIS C 326 PHE 0.025 0.001 PHE E 272 TYR 0.017 0.001 TYR B 97 ARG 0.002 0.000 ARG B 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.53 seconds wall clock time: 86 minutes 8.94 seconds (5168.94 seconds total)