Starting phenix.real_space_refine on Sat Feb 17 03:09:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whs_32510/02_2024/7whs_32510_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 10968 2.51 5 N 2946 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 221": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "F" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.48, per 1000 atoms: 0.55 Number of scatterers: 17232 At special positions: 0 Unit cell: (120.91, 118.77, 105.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 18 15.00 Mg 6 11.99 O 3192 8.00 N 2946 7.00 C 10968 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: 6.80 Conformation dependent library (CDL) restraints added in 3.3 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 37 sheets defined 19.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 69 through 76 removed outlier: 4.785A pdb=" N GLU A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.891A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 230 through 244 Proline residue: A 242 - end of helix Processing helix chain 'B' and resid 23 through 26 No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 69 through 72 No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 93 through 105 Proline residue: B 97 - end of helix removed outlier: 5.041A pdb=" N ASP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 230 through 244 Proline residue: B 242 - end of helix Processing helix chain 'C' and resid 23 through 26 No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 93 through 105 Proline residue: C 97 - end of helix removed outlier: 5.179A pdb=" N ASP C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 230 through 244 Proline residue: C 242 - end of helix Processing helix chain 'D' and resid 23 through 26 No H-bonds generated for 'chain 'D' and resid 23 through 26' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 41 through 52 Processing helix chain 'D' and resid 69 through 76 removed outlier: 4.660A pdb=" N GLU D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TRP D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 4.899A pdb=" N ASP D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 No H-bonds generated for 'chain 'D' and resid 149 through 152' Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 230 through 244 Proline residue: D 242 - end of helix Processing helix chain 'E' and resid 23 through 26 No H-bonds generated for 'chain 'E' and resid 23 through 26' Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'E' and resid 69 through 72 No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 93 through 105 Proline residue: E 97 - end of helix removed outlier: 5.042A pdb=" N ASP E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 152 No H-bonds generated for 'chain 'E' and resid 149 through 152' Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 230 through 244 Proline residue: E 242 - end of helix Processing helix chain 'F' and resid 23 through 26 No H-bonds generated for 'chain 'F' and resid 23 through 26' Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 69 through 72 No H-bonds generated for 'chain 'F' and resid 69 through 72' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 93 through 105 Proline residue: F 97 - end of helix removed outlier: 5.170A pdb=" N ASP F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 152 No H-bonds generated for 'chain 'F' and resid 149 through 152' Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 205 through 212 Processing helix chain 'F' and resid 230 through 244 Proline residue: F 242 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= B, first strand: chain 'A' and resid 119 through 121 Processing sheet with id= C, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.610A pdb=" N ILE A 141 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU A 220 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A 143 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.555A pdb=" N ALA A 291 " --> pdb=" O LEU A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= F, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.531A pdb=" N GLY A 376 " --> pdb=" O LYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 56 through 59 Processing sheet with id= H, first strand: chain 'B' and resid 119 through 121 Processing sheet with id= I, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.612A pdb=" N ILE B 141 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 220 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 143 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.614A pdb=" N ALA B 291 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= L, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.569A pdb=" N GLY B 376 " --> pdb=" O LYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 56 through 59 Processing sheet with id= N, first strand: chain 'C' and resid 119 through 121 Processing sheet with id= O, first strand: chain 'C' and resid 217 through 219 removed outlier: 6.633A pdb=" N ILE C 141 " --> pdb=" O PHE C 218 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.489A pdb=" N ALA C 291 " --> pdb=" O LEU C 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= R, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.660A pdb=" N GLY C 376 " --> pdb=" O LYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 56 through 59 Processing sheet with id= T, first strand: chain 'D' and resid 119 through 121 Processing sheet with id= U, first strand: chain 'D' and resid 217 through 220 removed outlier: 6.596A pdb=" N ILE D 141 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU D 220 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL D 143 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 273 through 275 removed outlier: 6.574A pdb=" N ALA D 291 " --> pdb=" O LEU D 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= X, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.543A pdb=" N GLY D 376 " --> pdb=" O LYS D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 56 through 59 Processing sheet with id= Z, first strand: chain 'E' and resid 119 through 121 Processing sheet with id= AA, first strand: chain 'E' and resid 217 through 220 removed outlier: 6.621A pdb=" N ILE E 141 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 220 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 143 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 273 through 275 removed outlier: 6.654A pdb=" N ALA E 291 " --> pdb=" O LEU E 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 338 through 340 Processing sheet with id= AD, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.572A pdb=" N GLY E 376 " --> pdb=" O LYS E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 56 through 59 Processing sheet with id= AF, first strand: chain 'F' and resid 119 through 121 Processing sheet with id= AG, first strand: chain 'F' and resid 217 through 219 removed outlier: 6.648A pdb=" N ILE F 141 " --> pdb=" O PHE F 218 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 267 through 269 removed outlier: 6.230A pdb=" N ALA F 285 " --> pdb=" O THR F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 273 through 275 removed outlier: 6.473A pdb=" N ALA F 291 " --> pdb=" O LEU F 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 338 through 340 Processing sheet with id= AK, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.654A pdb=" N GLY F 376 " --> pdb=" O LYS F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 266 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2977 1.32 - 1.44: 4309 1.44 - 1.57: 10114 1.57 - 1.69: 30 1.69 - 1.81: 174 Bond restraints: 17604 Sorted by residual: bond pdb=" C5 GTP B 401 " pdb=" C6 GTP B 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 GTP E 401 " pdb=" C6 GTP E 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 GTP F 401 " pdb=" C6 GTP F 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 GTP C 401 " pdb=" C6 GTP C 401 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 17599 not shown) Histogram of bond angle deviations from ideal: 96.15 - 104.21: 379 104.21 - 112.27: 8827 112.27 - 120.33: 7223 120.33 - 128.39: 7272 128.39 - 136.45: 173 Bond angle restraints: 23874 Sorted by residual: angle pdb=" N ILE C 201 " pdb=" CA ILE C 201 " pdb=" C ILE C 201 " ideal model delta sigma weight residual 109.37 96.15 13.22 1.35e+00 5.49e-01 9.59e+01 angle pdb=" N GLU F 202 " pdb=" CA GLU F 202 " pdb=" C GLU F 202 " ideal model delta sigma weight residual 111.36 118.36 -7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" N GLU E 202 " pdb=" CA GLU E 202 " pdb=" C GLU E 202 " ideal model delta sigma weight residual 111.28 117.28 -6.00 1.09e+00 8.42e-01 3.03e+01 angle pdb=" N GLU B 202 " pdb=" CA GLU B 202 " pdb=" C GLU B 202 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N SER C 200 " pdb=" CA SER C 200 " pdb=" C SER C 200 " ideal model delta sigma weight residual 107.70 118.86 -11.16 2.09e+00 2.29e-01 2.85e+01 ... (remaining 23869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 10291 34.20 - 68.40: 221 68.40 - 102.61: 6 102.61 - 136.81: 6 136.81 - 171.01: 12 Dihedral angle restraints: 10536 sinusoidal: 4332 harmonic: 6204 Sorted by residual: dihedral pdb=" C5' GTP C 401 " pdb=" O5' GTP C 401 " pdb=" PA GTP C 401 " pdb=" O3A GTP C 401 " ideal model delta sinusoidal sigma weight residual 69.27 -101.74 171.01 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP F 401 " pdb=" O5' GTP F 401 " pdb=" PA GTP F 401 " pdb=" O3A GTP F 401 " ideal model delta sinusoidal sigma weight residual 69.27 -100.85 170.12 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -100.44 169.71 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2399 0.098 - 0.197: 234 0.197 - 0.295: 17 0.295 - 0.394: 0 0.394 - 0.492: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.93 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA GLU C 202 " pdb=" N GLU C 202 " pdb=" C GLU C 202 " pdb=" CB GLU C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2649 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 199 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ALA C 199 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA C 199 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 200 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 110 " -0.050 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO B 111 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 110 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO E 111 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 111 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 111 " 0.041 5.00e-02 4.00e+02 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1277 2.74 - 3.28: 17490 3.28 - 3.82: 28438 3.82 - 4.36: 36030 4.36 - 4.90: 61898 Nonbonded interactions: 145133 Sorted by model distance: nonbonded pdb=" OG SER B 325 " pdb=" O SER B 343 " model vdw 2.197 2.440 nonbonded pdb=" OG SER C 325 " pdb=" O SER C 343 " model vdw 2.205 2.440 nonbonded pdb=" OG SER E 325 " pdb=" O SER E 343 " model vdw 2.206 2.440 nonbonded pdb=" OG SER F 325 " pdb=" O SER F 343 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP B 226 " pdb="MG MG B 402 " model vdw 2.217 2.170 ... (remaining 145128 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.520 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 46.050 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.005 0.076 17604 Z= 0.308 Angle : 0.783 13.220 23874 Z= 0.400 Chirality : 0.056 0.492 2652 Planarity : 0.006 0.076 3054 Dihedral : 16.308 171.012 6564 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 0.33 % Allowed : 0.60 % Favored : 99.08 % Cbeta Deviations : 0.05 % 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: -1.09 (0.18), residues: 2172 helix: 1.02 (0.30), residues: 318 sheet: 0.22 (0.35), residues: 234 loop : -1.33 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 149 HIS 0.009 0.002 HIS E 338 PHE 0.014 0.001 PHE D 85 TYR 0.007 0.001 TYR C 233 ARG 0.003 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6731 (m-40) cc_final: 0.6464 (m110) REVERT: C 144 SER cc_start: 0.8463 (t) cc_final: 0.8082 (p) REVERT: C 201 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 187 ASN cc_start: 0.6743 (m-40) cc_final: 0.6490 (m110) REVERT: F 102 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7023 (ttm110) REVERT: F 144 SER cc_start: 0.8449 (t) cc_final: 0.8077 (p) outliers start: 6 outliers final: 4 residues processed: 233 average time/residue: 0.2756 time to fit residues: 99.0495 Evaluate side-chains 211 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 196 optimal weight: 0.0170 overall best weight: 2.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17604 Z= 0.416 Angle : 0.685 6.224 23874 Z= 0.340 Chirality : 0.055 0.224 2652 Planarity : 0.006 0.053 3054 Dihedral : 14.973 167.012 2440 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.92 % Allowed : 8.85 % Favored : 90.23 % 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: -1.36 (0.17), residues: 2172 helix: 0.39 (0.28), residues: 354 sheet: 0.04 (0.34), residues: 234 loop : -1.47 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 336 HIS 0.008 0.002 HIS A 338 PHE 0.014 0.002 PHE D 85 TYR 0.013 0.002 TYR A 63 ARG 0.003 0.000 ARG E 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7129 (ttm110) REVERT: C 201 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.6649 (mt) REVERT: F 102 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7053 (ttm110) outliers start: 17 outliers final: 12 residues processed: 216 average time/residue: 0.2882 time to fit residues: 94.9628 Evaluate side-chains 213 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 163 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 0.0370 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17604 Z= 0.157 Angle : 0.559 6.366 23874 Z= 0.280 Chirality : 0.050 0.159 2652 Planarity : 0.005 0.050 3054 Dihedral : 14.659 170.750 2440 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.25 % Allowed : 11.24 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2172 helix: 0.52 (0.29), residues: 354 sheet: 0.16 (0.40), residues: 174 loop : -1.37 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 75 HIS 0.006 0.001 HIS E 261 PHE 0.008 0.001 PHE B 206 TYR 0.008 0.001 TYR F 157 ARG 0.004 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6153 (OUTLIER) cc_final: 0.5926 (t) REVERT: B 87 VAL cc_start: 0.6278 (OUTLIER) cc_final: 0.6073 (t) REVERT: B 221 GLU cc_start: 0.7920 (pm20) cc_final: 0.7483 (mm-30) REVERT: C 41 MET cc_start: 0.7814 (mtt) cc_final: 0.7545 (mtt) REVERT: C 87 VAL cc_start: 0.6030 (OUTLIER) cc_final: 0.5790 (t) REVERT: D 87 VAL cc_start: 0.6132 (OUTLIER) cc_final: 0.5880 (t) REVERT: D 221 GLU cc_start: 0.7789 (pm20) cc_final: 0.7211 (mm-30) REVERT: E 87 VAL cc_start: 0.6275 (OUTLIER) cc_final: 0.6067 (t) outliers start: 23 outliers final: 13 residues processed: 219 average time/residue: 0.2863 time to fit residues: 95.9037 Evaluate side-chains 209 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.0270 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17604 Z= 0.188 Angle : 0.556 6.046 23874 Z= 0.277 Chirality : 0.050 0.187 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.501 173.393 2438 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.17 % Allowed : 11.45 % Favored : 86.37 % 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: -1.23 (0.18), residues: 2172 helix: 0.61 (0.29), residues: 354 sheet: 0.12 (0.40), residues: 174 loop : -1.35 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.008 0.001 HIS B 261 PHE 0.007 0.001 PHE D 85 TYR 0.009 0.001 TYR E 157 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6093 (OUTLIER) cc_final: 0.5873 (t) REVERT: B 87 VAL cc_start: 0.6079 (OUTLIER) cc_final: 0.5859 (t) REVERT: B 353 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: C 353 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: D 87 VAL cc_start: 0.6199 (OUTLIER) cc_final: 0.5965 (t) REVERT: D 231 LYS cc_start: 0.7770 (tttp) cc_final: 0.7405 (pttt) REVERT: E 87 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5888 (t) REVERT: E 353 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: F 353 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8381 (m-30) outliers start: 40 outliers final: 24 residues processed: 222 average time/residue: 0.2785 time to fit residues: 94.8084 Evaluate side-chains 220 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 353 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 HIS ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17604 Z= 0.404 Angle : 0.643 5.874 23874 Z= 0.321 Chirality : 0.054 0.195 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.492 173.677 2438 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.28 % Allowed : 12.21 % Favored : 85.50 % 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 (0.18), residues: 2172 helix: 0.56 (0.30), residues: 330 sheet: -0.01 (0.34), residues: 234 loop : -1.45 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 336 HIS 0.020 0.002 HIS E 261 PHE 0.010 0.001 PHE D 85 TYR 0.013 0.002 TYR B 233 ARG 0.004 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8417 (ttp) cc_final: 0.8179 (ttp) REVERT: B 87 VAL cc_start: 0.6120 (OUTLIER) cc_final: 0.5895 (t) REVERT: B 231 LYS cc_start: 0.7793 (tttm) cc_final: 0.7586 (tttp) REVERT: B 353 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: C 353 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: E 87 VAL cc_start: 0.6108 (OUTLIER) cc_final: 0.5887 (t) REVERT: E 353 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: F 353 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8389 (m-30) outliers start: 42 outliers final: 28 residues processed: 232 average time/residue: 0.2986 time to fit residues: 104.0965 Evaluate side-chains 227 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Chi-restraints excluded: chain F residue 353 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 0.0030 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17604 Z= 0.154 Angle : 0.553 7.310 23874 Z= 0.276 Chirality : 0.049 0.167 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.346 175.531 2438 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.85 % Allowed : 13.95 % Favored : 84.20 % 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: -1.29 (0.18), residues: 2172 helix: 0.58 (0.29), residues: 354 sheet: 0.05 (0.39), residues: 174 loop : -1.40 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 75 HIS 0.007 0.001 HIS C 338 PHE 0.006 0.001 PHE E 167 TYR 0.013 0.001 TYR E 157 ARG 0.012 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.6071 (OUTLIER) cc_final: 0.5867 (t) REVERT: C 168 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7902 (p) REVERT: E 87 VAL cc_start: 0.6059 (OUTLIER) cc_final: 0.5855 (t) REVERT: E 353 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: F 144 SER cc_start: 0.8363 (t) cc_final: 0.8095 (p) outliers start: 34 outliers final: 25 residues processed: 217 average time/residue: 0.2903 time to fit residues: 96.1726 Evaluate side-chains 211 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17604 Z= 0.266 Angle : 0.576 6.644 23874 Z= 0.286 Chirality : 0.051 0.176 2652 Planarity : 0.005 0.047 3054 Dihedral : 14.270 177.141 2438 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.33 % Allowed : 13.68 % Favored : 83.98 % 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 (0.18), residues: 2172 helix: 0.56 (0.29), residues: 354 sheet: 0.20 (0.36), residues: 204 loop : -1.42 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 336 HIS 0.004 0.001 HIS B 261 PHE 0.008 0.001 PHE D 85 TYR 0.011 0.001 TYR B 233 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.6142 (OUTLIER) cc_final: 0.5932 (t) REVERT: B 353 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: C 168 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 353 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: D 231 LYS cc_start: 0.7683 (tttp) cc_final: 0.7346 (pttt) REVERT: E 87 VAL cc_start: 0.6131 (OUTLIER) cc_final: 0.5920 (t) REVERT: E 353 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: F 144 SER cc_start: 0.8381 (t) cc_final: 0.8100 (p) outliers start: 43 outliers final: 32 residues processed: 222 average time/residue: 0.3002 time to fit residues: 100.5308 Evaluate side-chains 225 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 0.0060 chunk 124 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17604 Z= 0.202 Angle : 0.551 5.983 23874 Z= 0.274 Chirality : 0.050 0.172 2652 Planarity : 0.005 0.047 3054 Dihedral : 14.167 179.371 2438 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.44 % Allowed : 13.95 % Favored : 83.60 % 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: -1.30 (0.18), residues: 2172 helix: 0.60 (0.29), residues: 354 sheet: 0.05 (0.39), residues: 174 loop : -1.41 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS E 261 PHE 0.006 0.001 PHE A 186 TYR 0.009 0.001 TYR B 233 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.6125 (OUTLIER) cc_final: 0.5911 (t) REVERT: B 126 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5749 (pp30) REVERT: B 353 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: C 168 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (p) REVERT: C 353 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: D 231 LYS cc_start: 0.7665 (tttp) cc_final: 0.7440 (pttp) REVERT: E 87 VAL cc_start: 0.6113 (OUTLIER) cc_final: 0.5905 (t) REVERT: E 353 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: F 144 SER cc_start: 0.8410 (t) cc_final: 0.8146 (p) REVERT: F 353 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8374 (m-30) outliers start: 45 outliers final: 32 residues processed: 230 average time/residue: 0.2911 time to fit residues: 101.3879 Evaluate side-chains 227 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 338 HIS Chi-restraints excluded: chain F residue 353 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 152 optimal weight: 0.0060 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17604 Z= 0.215 Angle : 0.557 5.993 23874 Z= 0.276 Chirality : 0.050 0.173 2652 Planarity : 0.005 0.047 3054 Dihedral : 14.084 179.968 2438 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.50 % Allowed : 14.12 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2172 helix: 0.61 (0.29), residues: 354 sheet: 0.04 (0.39), residues: 174 loop : -1.42 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.004 0.001 HIS B 261 PHE 0.007 0.001 PHE A 186 TYR 0.010 0.001 TYR B 233 ARG 0.002 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.6108 (OUTLIER) cc_final: 0.5889 (t) REVERT: B 126 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5821 (pp30) REVERT: B 353 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: C 168 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7916 (p) REVERT: C 353 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: D 231 LYS cc_start: 0.7664 (tttp) cc_final: 0.7386 (pttp) REVERT: E 87 VAL cc_start: 0.6126 (OUTLIER) cc_final: 0.5902 (t) REVERT: E 126 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5816 (pp30) REVERT: E 353 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: F 126 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5646 (pp30) REVERT: F 144 SER cc_start: 0.8407 (t) cc_final: 0.8152 (p) REVERT: F 168 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (p) REVERT: F 353 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8399 (m-30) outliers start: 46 outliers final: 33 residues processed: 231 average time/residue: 0.3051 time to fit residues: 105.4031 Evaluate side-chains 234 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 338 HIS Chi-restraints excluded: chain F residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17604 Z= 0.206 Angle : 0.556 6.163 23874 Z= 0.276 Chirality : 0.050 0.176 2652 Planarity : 0.005 0.047 3054 Dihedral : 13.975 178.728 2438 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.50 % Allowed : 14.33 % Favored : 83.17 % 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: -1.37 (0.18), residues: 2172 helix: 0.64 (0.29), residues: 354 sheet: -0.63 (0.36), residues: 204 loop : -1.40 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.004 0.001 HIS B 261 PHE 0.006 0.001 PHE A 85 TYR 0.009 0.001 TYR B 233 ARG 0.006 0.000 ARG C 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6400 (tt0) cc_final: 0.5987 (tt0) REVERT: B 87 VAL cc_start: 0.6106 (OUTLIER) cc_final: 0.5891 (t) REVERT: B 126 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5820 (pp30) REVERT: C 168 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 353 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: E 87 VAL cc_start: 0.6100 (OUTLIER) cc_final: 0.5878 (t) REVERT: E 126 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5863 (pp30) REVERT: F 126 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.5642 (pp30) REVERT: F 144 SER cc_start: 0.8415 (t) cc_final: 0.8158 (p) REVERT: F 168 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7986 (p) REVERT: F 353 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8395 (m-30) outliers start: 46 outliers final: 35 residues processed: 230 average time/residue: 0.3059 time to fit residues: 105.5759 Evaluate side-chains 232 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 338 HIS Chi-restraints excluded: chain F residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 158 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 150 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN E 261 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153421 restraints weight = 17411.667| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.12 r_work: 0.3423 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17604 Z= 0.161 Angle : 0.542 6.305 23874 Z= 0.270 Chirality : 0.050 0.236 2652 Planarity : 0.004 0.047 3054 Dihedral : 13.911 179.616 2438 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.39 % Allowed : 14.50 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2172 helix: 0.67 (0.30), residues: 354 sheet: -0.61 (0.36), residues: 204 loop : -1.37 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 75 HIS 0.010 0.001 HIS E 261 PHE 0.006 0.001 PHE B 113 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.000 ARG E 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.05 seconds wall clock time: 63 minutes 10.31 seconds (3790.31 seconds total)