Starting phenix.real_space_refine on Sat Dec 9 15:18:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/12_2023/7e27_30953_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/12_2023/7e27_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_30953/12_2023/7e27_30953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/12_2023/7e27_30953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/12_2023/7e27_30953_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e27_30953/12_2023/7e27_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.31, per 1000 atoms: 0.55 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: 4.58 Conformation dependent library (CDL) restraints added in 2.4 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: 1.90 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: 3.51 Time building geometry restraints manager: 4.97 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: 3.170 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: 0.010 Extract box with map and model: 10.240 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 33.830 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.660 ------------------------------------------------------------------------------- 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 : 1.230 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 169 average time/residue: 1.3589 time to fit residues: 247.0099 Evaluate side-chains 133 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2531 time to fit residues: 2.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11680 Z= 0.153 Angle : 0.489 6.855 15850 Z= 0.272 Chirality : 0.038 0.139 1790 Planarity : 0.003 0.023 1930 Dihedral : 4.939 41.814 1595 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.20 % Allowed : 9.83 % Favored : 87.97 % 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: 0.04 (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 0.015 0.001 TYR A 236 ARG 0.001 0.000 ARG B 27 *********************** 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 165 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.291 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 155 average time/residue: 1.3399 time to fit residues: 224.2315 Evaluate side-chains 156 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 1.4670 time to fit residues: 12.5891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11680 Z= 0.367 Angle : 0.661 7.420 15850 Z= 0.367 Chirality : 0.049 0.218 1790 Planarity : 0.004 0.025 1930 Dihedral : 5.361 35.626 1595 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.56 % Allowed : 8.81 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1425 helix: 0.94 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 284 PHE 0.029 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 185 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 1.301 Fit side-chains outliers start: 42 outliers final: 21 residues processed: 173 average time/residue: 1.3620 time to fit residues: 254.8325 Evaluate side-chains 165 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 1.2050 time to fit residues: 6.9056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 0.0010 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.1919 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= 0.129 Angle : 0.474 6.619 15850 Z= 0.262 Chirality : 0.037 0.149 1790 Planarity : 0.003 0.018 1930 Dihedral : 4.616 31.642 1595 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.37 % Allowed : 11.19 % Favored : 86.44 % 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: 1.41 (0.22), residues: 1425 helix: 1.60 (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 0.026 0.001 PHE D 223 TYR 0.018 0.001 TYR A 286 ARG 0.001 0.000 ARG A 74 *********************** 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 174 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.207 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 168 average time/residue: 1.3492 time to fit residues: 244.6387 Evaluate side-chains 151 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 1.6680 time to fit residues: 5.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11680 Z= 0.337 Angle : 0.643 7.266 15850 Z= 0.356 Chirality : 0.048 0.201 1790 Planarity : 0.003 0.023 1930 Dihedral : 5.248 36.609 1595 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.05 % Allowed : 11.78 % 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: 1.07 (0.21), residues: 1425 helix: 1.30 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 284 PHE 0.026 0.003 PHE C 223 TYR 0.020 0.002 TYR A 236 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 171 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.307 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 163 average time/residue: 1.3164 time to fit residues: 232.1715 Evaluate side-chains 153 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 2.0890 time to fit residues: 3.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11680 Z= 0.197 Angle : 0.542 7.048 15850 Z= 0.301 Chirality : 0.041 0.161 1790 Planarity : 0.003 0.021 1930 Dihedral : 4.943 34.026 1595 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.54 % Allowed : 12.20 % Favored : 85.25 % 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: 1.37 (0.22), residues: 1425 helix: 1.53 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 59 PHE 0.023 0.002 PHE D 223 TYR 0.015 0.002 TYR D 236 ARG 0.001 0.000 ARG B 27 *********************** 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 163 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.813 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 156 average time/residue: 1.2756 time to fit residues: 215.6711 Evaluate side-chains 158 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 1.2579 time to fit residues: 5.6911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11680 Z= 0.255 Angle : 0.585 7.172 15850 Z= 0.325 Chirality : 0.044 0.165 1790 Planarity : 0.003 0.022 1930 Dihedral : 5.084 35.341 1595 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.71 % Allowed : 12.29 % Favored : 85.00 % 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: 1.28 (0.21), residues: 1425 helix: 1.45 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 284 PHE 0.024 0.002 PHE D 223 TYR 0.017 0.002 TYR A 236 ARG 0.001 0.000 ARG B 27 *********************** 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 169 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.312 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 162 average time/residue: 1.3831 time to fit residues: 241.9748 Evaluate side-chains 161 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.5239 time to fit residues: 3.2196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 265 ASN D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11680 Z= 0.265 Angle : 0.594 7.387 15850 Z= 0.329 Chirality : 0.044 0.165 1790 Planarity : 0.003 0.023 1930 Dihedral : 5.131 35.913 1595 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.88 % Allowed : 12.12 % Favored : 85.00 % 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: 1.24 (0.21), residues: 1425 helix: 1.42 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.49 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 284 PHE 0.023 0.002 PHE A 223 TYR 0.017 0.002 TYR A 236 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 171 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.253 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 162 average time/residue: 1.3271 time to fit residues: 231.9418 Evaluate side-chains 158 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 1.3859 time to fit residues: 7.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 132 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 C 265 ASN E 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11680 Z= 0.195 Angle : 0.539 7.056 15850 Z= 0.299 Chirality : 0.041 0.160 1790 Planarity : 0.003 0.022 1930 Dihedral : 4.904 33.909 1595 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 13.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1425 helix: 1.58 (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 0.022 0.002 PHE D 223 TYR 0.015 0.002 TYR A 236 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 155 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.284 Fit side-chains outliers start: 20 outliers final: 19 residues processed: 154 average time/residue: 1.3379 time to fit residues: 222.6958 Evaluate side-chains 149 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11680 Z= 0.140 Angle : 0.488 7.478 15850 Z= 0.269 Chirality : 0.038 0.152 1790 Planarity : 0.003 0.020 1930 Dihedral : 4.595 32.181 1595 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.61 % Allowed : 13.64 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1425 helix: 1.81 (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 0.022 0.001 PHE D 223 TYR 0.012 0.001 TYR C 236 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 153 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.340 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 153 average time/residue: 1.2599 time to fit residues: 209.2168 Evaluate side-chains 150 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 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 265 ASN D 265 ASN E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.083431 restraints weight = 12388.163| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.19 r_work: 0.2789 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1913 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= 0.286 Angle : 0.606 7.795 15850 Z= 0.336 Chirality : 0.046 0.168 1790 Planarity : 0.003 0.022 1930 Dihedral : 5.125 35.652 1595 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.03 % Allowed : 13.05 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1425 helix: 1.52 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 284 PHE 0.024 0.002 PHE D 223 TYR 0.018 0.002 TYR A 236 ARG 0.002 0.000 ARG D 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.77 seconds wall clock time: 76 minutes 55.95 seconds (4615.95 seconds total)