Starting phenix.real_space_refine on Thu Feb 15 06:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/02_2024/7e27_30953_updated.pdb" } resolution = 2.29 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= 0.005 sd= 0.129 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 S 70 5.16 5 C 7575 2.51 5 N 1765 2.21 5 O 2040 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E ARG 290": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11475 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 6.22, per 1000 atoms: 0.54 Number of scatterers: 11475 At special positions: 0 Unit cell: (96.4678, 95.7932, 81.6266, 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) S 70 16.00 F 25 9.00 O 2040 8.00 N 1765 7.00 C 7575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.1 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 0 sheets defined 74.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.976A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.810A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 100 Proline residue: A 91 - end of helix removed outlier: 5.249A pdb=" N PHE A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 4.453A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 147 Processing helix chain 'A' and resid 165 through 178 removed outlier: 3.562A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 205 removed outlier: 3.688A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.958A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 274 through 290 removed outlier: 5.960A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.975A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.810A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 Proline residue: B 91 - end of helix removed outlier: 5.249A pdb=" N PHE B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 4.453A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 147 Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.561A pdb=" N VAL B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 205 removed outlier: 3.688A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 removed outlier: 3.957A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 274 through 290 removed outlier: 5.959A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 removed outlier: 3.975A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 67 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.810A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 100 Proline residue: C 91 - end of helix removed outlier: 5.248A pdb=" N PHE C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 4.454A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 147 Processing helix chain 'C' and resid 165 through 178 removed outlier: 3.561A pdb=" N VAL C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 removed outlier: 3.688A pdb=" N PHE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 225 removed outlier: 3.958A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 274 through 290 removed outlier: 5.960A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 37 removed outlier: 3.976A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 67 Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.810A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 100 Proline residue: D 91 - end of helix removed outlier: 5.248A pdb=" N PHE D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 4.453A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 147 Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.560A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 205 removed outlier: 3.689A pdb=" N PHE D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.957A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 274 through 290 removed outlier: 5.959A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 37 removed outlier: 3.975A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 67 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.810A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 100 Proline residue: E 91 - end of helix removed outlier: 5.248A pdb=" N PHE E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 removed outlier: 4.454A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 147 Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.561A pdb=" N VAL E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 removed outlier: 3.688A pdb=" N PHE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.958A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 258 through 270 Processing helix chain 'E' and resid 274 through 290 removed outlier: 5.960A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2175 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: 3.26 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.43: 3560 1.43 - 1.56: 6340 1.56 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11680 Sorted by residual: bond pdb=" C12 HV6 B 401 " pdb=" O21 HV6 B 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C12 HV6 A 401 " pdb=" O21 HV6 A 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 C 401 " pdb=" O21 HV6 C 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 D 401 " pdb=" O21 HV6 D 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C12 HV6 E 401 " pdb=" O21 HV6 E 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 11675 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.44: 163 106.44 - 112.90: 5923 112.90 - 119.35: 3295 119.35 - 125.81: 6394 125.81 - 132.27: 75 Bond angle restraints: 15850 Sorted by residual: angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 109.81 120.12 -10.31 2.21e+00 2.05e-01 2.18e+01 angle pdb=" N PHE A 90 " pdb=" CA PHE A 90 " pdb=" C PHE A 90 " ideal model delta sigma weight residual 109.81 120.11 -10.30 2.21e+00 2.05e-01 2.17e+01 angle pdb=" N PHE B 90 " pdb=" CA PHE B 90 " pdb=" C PHE B 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE E 90 " pdb=" CA PHE E 90 " pdb=" C PHE E 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE C 90 " pdb=" CA PHE C 90 " pdb=" C PHE C 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 ... (remaining 15845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 5857 16.42 - 32.84: 608 32.84 - 49.27: 95 49.27 - 65.69: 40 65.69 - 82.11: 15 Dihedral angle restraints: 6615 sinusoidal: 2420 harmonic: 4195 Sorted by residual: dihedral pdb=" CA TYR E 70 " pdb=" C TYR E 70 " pdb=" N HIS E 71 " pdb=" CA HIS E 71 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR C 70 " pdb=" C TYR C 70 " pdb=" N HIS C 71 " pdb=" CA HIS C 71 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N HIS B 71 " pdb=" CA HIS B 71 " ideal model delta harmonic sigma weight residual 180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1508 0.068 - 0.137: 209 0.137 - 0.205: 38 0.205 - 0.273: 20 0.273 - 0.341: 15 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB VAL E 142 " pdb=" CA VAL E 142 " pdb=" CG1 VAL E 142 " pdb=" CG2 VAL E 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL C 142 " pdb=" CA VAL C 142 " pdb=" CG1 VAL C 142 " pdb=" CG2 VAL C 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB VAL A 142 " pdb=" CA VAL A 142 " pdb=" CG1 VAL A 142 " pdb=" CG2 VAL A 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1787 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR D 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR E 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 212 " -0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR B 212 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 212 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 212 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 212 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 212 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3939 2.84 - 3.35: 10856 3.35 - 3.87: 21582 3.87 - 4.38: 25626 4.38 - 4.90: 42019 Nonbonded interactions: 104022 Sorted by model distance: nonbonded pdb=" O ALA E 226 " pdb=" O HOH E 501 " model vdw 2.322 2.440 nonbonded pdb=" N ASP E 208 " pdb=" OD1 ASP E 208 " model vdw 2.331 2.520 nonbonded pdb=" N ASP B 208 " pdb=" OD1 ASP B 208 " model vdw 2.331 2.520 nonbonded pdb=" N ASP A 208 " pdb=" OD1 ASP A 208 " model vdw 2.331 2.520 nonbonded pdb=" N ASP D 208 " pdb=" OD1 ASP D 208 " model vdw 2.332 2.520 ... (remaining 104017 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: 2.170 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: 0.000 Extract box with map and model: 10.280 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.390 Find NCS groups from input model: 0.740 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.007 0.094 11680 Z= 0.474 Angle : 0.911 10.307 15850 Z= 0.513 Chirality : 0.061 0.341 1790 Planarity : 0.006 0.033 1930 Dihedral : 14.587 82.111 3965 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.42 % Allowed : 5.08 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 1425 helix: -1.34 (0.12), residues: 1145 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 59 PHE 0.042 0.004 PHE C 223 TYR 0.050 0.003 TYR B 212 ARG 0.001 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.244 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 169 average time/residue: 1.3317 time to fit residues: 242.0426 Evaluate side-chains 133 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain E residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 71 HIS B 265 ASN C 265 ASN D 265 ASN E 71 HIS E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11680 Z= 0.150 Angle : 0.489 6.971 15850 Z= 0.272 Chirality : 0.038 0.138 1790 Planarity : 0.003 0.022 1930 Dihedral : 4.936 41.898 1599 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.12 % Allowed : 9.58 % Favored : 88.31 % 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: 0.05 (0.20), residues: 1425 helix: 0.63 (0.14), residues: 1135 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 230 PHE 0.025 0.002 PHE B 223 TYR 0.016 0.001 TYR A 236 ARG 0.001 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.214 Fit side-chains REVERT: A 201 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 283 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6581 (pm20) REVERT: B 201 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: B 283 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6558 (pm20) REVERT: C 283 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6583 (pm20) REVERT: D 201 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: E 201 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: E 283 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6594 (pm20) outliers start: 25 outliers final: 12 residues processed: 154 average time/residue: 1.2991 time to fit residues: 216.0539 Evaluate side-chains 146 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 179 HIS A 265 ASN B 179 HIS B 265 ASN C 179 HIS C 265 ASN D 71 HIS D 179 HIS D 265 ASN E 179 HIS E 265 ASN E 284 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11680 Z= 0.353 Angle : 0.653 7.430 15850 Z= 0.362 Chirality : 0.049 0.215 1790 Planarity : 0.004 0.024 1930 Dihedral : 5.325 35.196 1595 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.64 % Allowed : 8.64 % Favored : 87.71 % 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: 0.56 (0.21), residues: 1425 helix: 0.96 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 284 PHE 0.028 0.003 PHE D 223 TYR 0.022 0.003 TYR A 236 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 1.259 Fit side-chains REVERT: A 201 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 283 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6424 (pm20) REVERT: B 201 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 283 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6510 (pm20) REVERT: C 283 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6547 (pm20) REVERT: D 201 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: D 223 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7222 (p90) REVERT: E 201 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7904 (m-80) outliers start: 43 outliers final: 25 residues processed: 162 average time/residue: 1.1742 time to fit residues: 206.9327 Evaluate side-chains 165 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.0070 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 234 ASN C 257 ASN C 265 ASN D 265 ASN E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11680 Z= 0.127 Angle : 0.469 6.604 15850 Z= 0.259 Chirality : 0.037 0.150 1790 Planarity : 0.003 0.018 1930 Dihedral : 4.605 32.129 1595 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.29 % Allowed : 11.19 % 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: 1.45 (0.22), residues: 1425 helix: 1.62 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 59 PHE 0.020 0.001 PHE E 223 TYR 0.018 0.001 TYR A 286 ARG 0.001 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.384 Fit side-chains REVERT: A 201 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: A 283 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6614 (pm20) REVERT: B 201 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 283 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6490 (pm20) REVERT: C 283 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6505 (pm20) REVERT: D 201 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: D 283 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6472 (pm20) REVERT: E 283 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6536 (pm20) outliers start: 27 outliers final: 12 residues processed: 156 average time/residue: 1.2816 time to fit residues: 216.7820 Evaluate side-chains 142 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 234 ASN C 257 ASN C 265 ASN D 265 ASN E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11680 Z= 0.284 Angle : 0.602 7.179 15850 Z= 0.334 Chirality : 0.045 0.180 1790 Planarity : 0.003 0.021 1930 Dihedral : 5.069 34.549 1595 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.54 % Allowed : 11.61 % Favored : 85.85 % 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: 1.22 (0.21), residues: 1425 helix: 1.42 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 284 PHE 0.026 0.002 PHE D 223 TYR 0.019 0.002 TYR A 286 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.382 Fit side-chains REVERT: A 201 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: A 283 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6560 (pm20) REVERT: B 201 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: B 283 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6469 (pm20) REVERT: C 283 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6506 (pm20) REVERT: D 201 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: E 201 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: E 283 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6581 (pm20) outliers start: 30 outliers final: 18 residues processed: 153 average time/residue: 1.2730 time to fit residues: 211.4288 Evaluate side-chains 151 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11680 Z= 0.309 Angle : 0.623 7.258 15850 Z= 0.346 Chirality : 0.047 0.199 1790 Planarity : 0.003 0.023 1930 Dihedral : 5.246 37.074 1595 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.22 % Allowed : 11.61 % Favored : 85.17 % 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: 1425 helix: 1.33 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 284 PHE 0.027 0.003 PHE D 223 TYR 0.021 0.002 TYR A 286 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.253 Fit side-chains REVERT: A 201 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 201 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 273 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8383 (mp) REVERT: B 283 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6531 (pm20) REVERT: C 283 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6405 (pm20) REVERT: D 201 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: E 201 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7879 (m-80) outliers start: 38 outliers final: 20 residues processed: 163 average time/residue: 1.2572 time to fit residues: 221.9235 Evaluate side-chains 159 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN C 234 ASN C 257 ASN C 265 ASN E 265 ASN E 284 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11680 Z= 0.178 Angle : 0.522 6.979 15850 Z= 0.290 Chirality : 0.040 0.156 1790 Planarity : 0.003 0.022 1930 Dihedral : 4.839 33.329 1595 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.80 % Allowed : 12.12 % Favored : 85.08 % 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: 1.51 (0.22), residues: 1425 helix: 1.63 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.48 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 59 PHE 0.023 0.002 PHE D 223 TYR 0.020 0.001 TYR A 286 ARG 0.001 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.265 Fit side-chains REVERT: A 201 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: B 201 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 283 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6541 (pm20) REVERT: C 283 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6460 (pm20) REVERT: D 173 ILE cc_start: 0.8613 (mm) cc_final: 0.8411 (mm) REVERT: D 201 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: E 283 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6459 (pm20) outliers start: 33 outliers final: 19 residues processed: 158 average time/residue: 1.2511 time to fit residues: 214.5952 Evaluate side-chains 156 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 234 ASN C 257 ASN C 265 ASN D 265 ASN E 265 ASN E 284 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11680 Z= 0.287 Angle : 0.606 7.227 15850 Z= 0.336 Chirality : 0.045 0.183 1790 Planarity : 0.003 0.023 1930 Dihedral : 5.155 35.938 1595 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.97 % Allowed : 12.20 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1425 helix: 1.44 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 284 PHE 0.026 0.002 PHE D 223 TYR 0.021 0.002 TYR A 286 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.303 Fit side-chains REVERT: A 201 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 201 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 283 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6457 (pm20) REVERT: C 283 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6425 (pm20) REVERT: D 201 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: E 201 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7867 (m-80) outliers start: 35 outliers final: 19 residues processed: 160 average time/residue: 1.2547 time to fit residues: 217.4933 Evaluate side-chains 155 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 234 ASN C 257 ASN C 265 ASN D 265 ASN E 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11680 Z= 0.241 Angle : 0.575 7.197 15850 Z= 0.319 Chirality : 0.043 0.164 1790 Planarity : 0.003 0.023 1930 Dihedral : 5.068 35.461 1595 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.03 % Allowed : 13.47 % Favored : 84.49 % 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: 1.35 (0.21), residues: 1425 helix: 1.50 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.46 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 284 PHE 0.026 0.002 PHE D 223 TYR 0.022 0.002 TYR A 286 ARG 0.001 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.146 Fit side-chains REVERT: A 201 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: B 201 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 283 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6498 (pm20) REVERT: C 283 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6491 (pm20) REVERT: D 201 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7854 (m-80) outliers start: 24 outliers final: 21 residues processed: 153 average time/residue: 1.2407 time to fit residues: 205.5998 Evaluate side-chains 156 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN C 257 ASN E 265 ASN E 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11680 Z= 0.146 Angle : 0.490 6.768 15850 Z= 0.271 Chirality : 0.038 0.154 1790 Planarity : 0.003 0.020 1930 Dihedral : 4.656 32.522 1595 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 13.90 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.22), residues: 1425 helix: 1.79 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 59 PHE 0.021 0.002 PHE D 223 TYR 0.021 0.001 TYR A 286 ARG 0.001 0.000 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.230 Fit side-chains REVERT: A 201 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 201 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 283 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6498 (pm20) REVERT: C 283 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6427 (pm20) REVERT: D 201 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: D 283 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6509 (pm20) REVERT: E 283 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6545 (pm20) outliers start: 20 outliers final: 15 residues processed: 146 average time/residue: 1.2948 time to fit residues: 204.5360 Evaluate side-chains 146 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 234 ASN C 257 ASN D 265 ASN E 265 ASN E 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.096124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.084098 restraints weight = 12338.573| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.21 r_work: 0.2800 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11680 Z= 0.251 Angle : 0.581 7.204 15850 Z= 0.322 Chirality : 0.044 0.165 1790 Planarity : 0.003 0.022 1930 Dihedral : 5.037 34.601 1595 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.95 % Allowed : 13.47 % Favored : 84.58 % 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: 1.42 (0.21), residues: 1425 helix: 1.55 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.46 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 284 PHE 0.025 0.002 PHE D 223 TYR 0.017 0.002 TYR A 236 ARG 0.001 0.000 ARG D 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.42 seconds wall clock time: 71 minutes 13.30 seconds (4273.30 seconds total)