Starting phenix.real_space_refine on Sun Mar 17 21:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/03_2024/7sjn_25162.pdb" } resolution = 3.4 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= 0.078 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 18 5.16 5 C 6069 2.51 5 N 1611 2.21 5 O 1881 1.98 5 H 9483 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 56": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19062 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "B" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "C" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 9.10, per 1000 atoms: 0.48 Number of scatterers: 19062 At special positions: 0 Unit cell: (136.8, 136.8, 98.4, 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 18 16.00 O 1881 8.00 N 1611 7.00 C 6069 6.00 H 9483 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.98 Conformation dependent library (CDL) restraints added in 2.1 seconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 25 sheets defined 8.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 170 through 180 removed outlier: 4.130A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.963A pdb=" N ILE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'C' and resid 171 through 179 removed outlier: 3.607A pdb=" N VAL C 175 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 357 through 367 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.610A pdb=" N SER F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.592A pdb=" N PHE G 82 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.638A pdb=" N ASP H 31 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.714A pdb=" N GLU H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.021A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 203 removed outlier: 6.612A pdb=" N LEU A 188 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A 203 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 186 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 228 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 242 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS A 255 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 296 removed outlier: 4.047A pdb=" N THR A 291 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 282 " --> pdb=" O PRO A 331 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 332 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.795A pdb=" N PHE B 207 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 255 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE B 242 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 292 through 296 removed outlier: 3.506A pdb=" N ILE B 282 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 332 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR B 344 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 355 " --> pdb=" O THR B 344 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS B 346 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 353 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.594A pdb=" N VAL C 199 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 188 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 203 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 186 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.594A pdb=" N VAL C 199 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 188 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 203 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 186 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 207 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS C 255 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE C 242 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 292 through 296 removed outlier: 3.588A pdb=" N GLY C 341 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN C 334 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 339 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 344 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE C 353 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS C 346 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE C 351 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.636A pdb=" N LEU D 83 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.643A pdb=" N GLU D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.613A pdb=" N TYR D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.909A pdb=" N LEU E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 61 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 89 removed outlier: 3.825A pdb=" N GLN E 89 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.566A pdb=" N GLU F 10 " --> pdb=" O THR F 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 59 through 60 removed outlier: 5.328A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.564A pdb=" N VAL G 19 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.012A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 83 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP G 34 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.012A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 83 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN G 89 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR G 96 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.614A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 60 removed outlier: 4.378A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP H 52 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.639A pdb=" N PHE L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.329A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 732 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: 6.97 Time building geometry restraints manager: 16.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9483 1.02 - 1.22: 4 1.22 - 1.42: 4059 1.42 - 1.62: 5687 1.62 - 1.82: 24 Bond restraints: 19257 Sorted by residual: bond pdb=" ND2 ASN E 52 " pdb="HD21 ASN E 52 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN E 52 " pdb="HD22 ASN E 52 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" NE ARG B 197 " pdb=" HE ARG B 197 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG B 166 " pdb=" HE ARG B 166 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG F 87 " pdb=" HE ARG F 87 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 ... (remaining 19252 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.24: 275 106.24 - 113.50: 23238 113.50 - 120.76: 6275 120.76 - 128.02: 4926 128.02 - 135.28: 107 Bond angle restraints: 34821 Sorted by residual: angle pdb=" C THR D 113 " pdb=" CA THR D 113 " pdb=" CB THR D 113 " ideal model delta sigma weight residual 111.17 101.46 9.71 1.54e+00 4.22e-01 3.97e+01 angle pdb=" C SER D 7 " pdb=" N GLY D 8 " pdb=" CA GLY D 8 " ideal model delta sigma weight residual 121.01 129.52 -8.51 1.42e+00 4.96e-01 3.59e+01 angle pdb=" N ARG B 190 " pdb=" CA ARG B 190 " pdb=" C ARG B 190 " ideal model delta sigma weight residual 111.04 102.80 8.24 1.55e+00 4.16e-01 2.82e+01 angle pdb=" N ALA D 58 " pdb=" CA ALA D 58 " pdb=" C ALA D 58 " ideal model delta sigma weight residual 108.76 117.59 -8.83 1.69e+00 3.50e-01 2.73e+01 angle pdb=" C LYS B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta sigma weight residual 121.80 133.51 -11.71 2.44e+00 1.68e-01 2.30e+01 ... (remaining 34816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 8256 17.28 - 34.57: 637 34.57 - 51.85: 168 51.85 - 69.13: 41 69.13 - 86.42: 9 Dihedral angle restraints: 9111 sinusoidal: 4944 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.28 49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" C THR D 113 " pdb=" N THR D 113 " pdb=" CA THR D 113 " pdb=" CB THR D 113 " ideal model delta harmonic sigma weight residual -122.00 -109.47 -12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" N LYS B 196 " pdb=" C LYS B 196 " pdb=" CA LYS B 196 " pdb=" CB LYS B 196 " ideal model delta harmonic sigma weight residual 122.80 133.94 -11.14 0 2.50e+00 1.60e-01 1.99e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1317 0.072 - 0.143: 189 0.143 - 0.215: 8 0.215 - 0.286: 3 0.286 - 0.358: 1 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA LYS B 196 " pdb=" N LYS B 196 " pdb=" C LYS B 196 " pdb=" CB LYS B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA THR D 113 " pdb=" N THR D 113 " pdb=" C THR D 113 " pdb=" CB THR D 113 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER B 195 " pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CB SER B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1515 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 194 " 0.023 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" N SER B 195 " -0.075 2.00e-02 2.50e+03 pdb=" CA SER B 195 " 0.018 2.00e-02 2.50e+03 pdb=" H SER B 195 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 3 " 0.032 2.00e-02 2.50e+03 3.47e-02 1.81e+01 pdb=" CD GLN H 3 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN H 3 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN H 3 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN H 3 " -0.051 2.00e-02 2.50e+03 pdb="HE22 GLN H 3 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 3 " -0.030 2.00e-02 2.50e+03 3.18e-02 1.52e+01 pdb=" CD GLN L 3 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN L 3 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 GLN L 3 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN L 3 " -0.048 2.00e-02 2.50e+03 pdb="HE22 GLN L 3 " 0.046 2.00e-02 2.50e+03 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 744 2.17 - 2.77: 37471 2.77 - 3.38: 49626 3.38 - 3.99: 66222 3.99 - 4.60: 102224 Nonbonded interactions: 256287 Sorted by model distance: nonbonded pdb=" HB2 PRO B 193 " pdb=" HZ2 TRP E 95 " model vdw 1.557 2.270 nonbonded pdb=" OD1 ASP D 101 " pdb=" H TYR D 102 " model vdw 1.601 1.850 nonbonded pdb=" O CYS D 96 " pdb=" H GLY D 110 " model vdw 1.636 1.850 nonbonded pdb="HH11 ARG B 190 " pdb=" HE1 TYR D 100 " model vdw 1.643 2.100 nonbonded pdb="HH21 ARG B 227 " pdb=" OD2 ASP D 101 " model vdw 1.646 1.850 ... (remaining 256282 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' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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: 1.220 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: 0.310 Extract box with map and model: 5.950 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 63.840 Find NCS groups from input model: 0.920 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.004 0.088 9774 Z= 0.233 Angle : 0.649 11.712 13263 Z= 0.385 Chirality : 0.049 0.358 1518 Planarity : 0.004 0.085 1692 Dihedral : 12.762 86.418 3528 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 8.77 % 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: -0.44 (0.26), residues: 1227 helix: 1.42 (0.73), residues: 66 sheet: -0.49 (0.24), residues: 520 loop : -0.16 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 95 HIS 0.003 0.001 HIS D 35 PHE 0.018 0.001 PHE L 97 TYR 0.010 0.001 TYR E 35 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 ILE cc_start: 0.8209 (mm) cc_final: 0.7603 (mm) REVERT: D 73 ASP cc_start: 0.6245 (t0) cc_final: 0.5892 (t0) REVERT: D 116 THR cc_start: 0.8581 (m) cc_final: 0.8347 (p) REVERT: E 4 MET cc_start: 0.6851 (mtp) cc_final: 0.5552 (mtp) REVERT: F 47 TRP cc_start: 0.7317 (t60) cc_final: 0.6602 (t60) REVERT: G 96 THR cc_start: 0.8058 (p) cc_final: 0.7721 (t) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.5446 time to fit residues: 146.1265 Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN E 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.223 Angle : 0.515 4.547 13263 Z= 0.275 Chirality : 0.046 0.157 1518 Planarity : 0.003 0.043 1692 Dihedral : 3.977 17.250 1329 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.38 % Allowed : 8.14 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.38 (0.25), residues: 1227 helix: 1.54 (0.71), residues: 66 sheet: -0.34 (0.24), residues: 514 loop : -0.23 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 90 HIS 0.004 0.001 HIS F 35 PHE 0.011 0.001 PHE L 82 TYR 0.012 0.001 TYR F 80 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 ILE cc_start: 0.8229 (mm) cc_final: 0.7983 (mm) REVERT: D 73 ASP cc_start: 0.6106 (t0) cc_final: 0.5704 (t0) REVERT: D 90 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: F 47 TRP cc_start: 0.7322 (t60) cc_final: 0.6676 (t60) REVERT: G 4 MET cc_start: 0.8783 (mmp) cc_final: 0.8506 (mmp) outliers start: 4 outliers final: 3 residues processed: 172 average time/residue: 0.5489 time to fit residues: 125.7439 Evaluate side-chains 150 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9774 Z= 0.315 Angle : 0.539 4.751 13263 Z= 0.287 Chirality : 0.046 0.164 1518 Planarity : 0.004 0.031 1692 Dihedral : 4.210 23.604 1329 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.33 % Allowed : 10.13 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.25), residues: 1227 helix: 1.08 (0.68), residues: 72 sheet: -0.42 (0.24), residues: 488 loop : -0.34 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 90 HIS 0.005 0.001 HIS B 185 PHE 0.014 0.001 PHE A 171 TYR 0.017 0.001 TYR L 86 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7749 (t0) cc_final: 0.7490 (t0) REVERT: D 28 LYS cc_start: 0.6392 (ttpt) cc_final: 0.5975 (ttpt) REVERT: D 34 MET cc_start: 0.7203 (mmm) cc_final: 0.6945 (mmm) REVERT: D 48 ILE cc_start: 0.6446 (mt) cc_final: 0.6237 (mt) REVERT: D 73 ASP cc_start: 0.5939 (t0) cc_final: 0.5601 (t0) REVERT: E 46 LEU cc_start: 0.8254 (tp) cc_final: 0.8011 (mt) REVERT: E 88 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6561 (tp-100) REVERT: F 47 TRP cc_start: 0.7476 (t60) cc_final: 0.6836 (t60) REVERT: G 4 MET cc_start: 0.8632 (mmp) cc_final: 0.8320 (mmp) REVERT: H 111 GLN cc_start: 0.7871 (pm20) cc_final: 0.7618 (pm20) outliers start: 14 outliers final: 12 residues processed: 157 average time/residue: 0.5532 time to fit residues: 116.1123 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.232 Angle : 0.498 4.666 13263 Z= 0.262 Chirality : 0.046 0.159 1518 Planarity : 0.003 0.029 1692 Dihedral : 4.079 22.887 1329 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.42 % Allowed : 11.46 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.49 (0.25), residues: 1227 helix: 1.13 (0.68), residues: 72 sheet: -0.40 (0.24), residues: 488 loop : -0.32 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 PHE 0.011 0.001 PHE E 97 TYR 0.010 0.001 TYR F 95 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7760 (t0) cc_final: 0.7483 (t0) REVERT: D 28 LYS cc_start: 0.6211 (ttpt) cc_final: 0.5861 (ttpt) REVERT: D 73 ASP cc_start: 0.5888 (t0) cc_final: 0.5527 (t0) REVERT: F 47 TRP cc_start: 0.7365 (t60) cc_final: 0.6788 (t60) REVERT: G 4 MET cc_start: 0.8570 (mmp) cc_final: 0.8253 (mmp) REVERT: H 111 GLN cc_start: 0.7873 (pm20) cc_final: 0.7586 (pm20) REVERT: L 3 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8010 (tm-30) outliers start: 15 outliers final: 15 residues processed: 156 average time/residue: 0.5701 time to fit residues: 118.9020 Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain L residue 81 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9774 Z= 0.404 Angle : 0.579 4.992 13263 Z= 0.310 Chirality : 0.048 0.169 1518 Planarity : 0.004 0.036 1692 Dihedral : 4.554 27.422 1329 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.80 % Allowed : 13.73 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.81 (0.24), residues: 1227 helix: 0.63 (0.66), residues: 72 sheet: -0.54 (0.23), residues: 521 loop : -0.55 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 90 HIS 0.006 0.002 HIS B 185 PHE 0.017 0.002 PHE A 171 TYR 0.017 0.002 TYR F 95 ARG 0.004 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7762 (t0) cc_final: 0.7495 (t0) REVERT: D 23 LYS cc_start: 0.8233 (tptt) cc_final: 0.7957 (tptm) REVERT: D 28 LYS cc_start: 0.6564 (ttpt) cc_final: 0.6191 (ttpt) REVERT: D 70 ILE cc_start: 0.7848 (mm) cc_final: 0.7329 (mm) REVERT: D 73 ASP cc_start: 0.6063 (t0) cc_final: 0.5648 (t0) REVERT: D 90 ASP cc_start: 0.7672 (t0) cc_final: 0.7252 (m-30) REVERT: F 47 TRP cc_start: 0.7545 (t60) cc_final: 0.7020 (t60) REVERT: G 4 MET cc_start: 0.8600 (mmp) cc_final: 0.8211 (mmp) REVERT: H 111 GLN cc_start: 0.7995 (pm20) cc_final: 0.7660 (pm20) outliers start: 19 outliers final: 17 residues processed: 156 average time/residue: 0.5519 time to fit residues: 115.6128 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.185 Angle : 0.489 4.611 13263 Z= 0.256 Chirality : 0.046 0.157 1518 Planarity : 0.003 0.029 1692 Dihedral : 4.154 24.806 1329 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.33 % Allowed : 14.68 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.62 (0.25), residues: 1227 helix: 1.33 (0.69), residues: 69 sheet: -0.53 (0.23), residues: 540 loop : -0.36 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 PHE 0.010 0.001 PHE A 194 TYR 0.009 0.001 TYR F 95 ARG 0.004 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7668 (t0) cc_final: 0.7391 (t0) REVERT: D 23 LYS cc_start: 0.8190 (tptt) cc_final: 0.7847 (tptm) REVERT: D 28 LYS cc_start: 0.6528 (ttpt) cc_final: 0.6206 (ttpt) REVERT: D 73 ASP cc_start: 0.6038 (t0) cc_final: 0.5618 (t0) REVERT: D 90 ASP cc_start: 0.7503 (t0) cc_final: 0.7081 (m-30) REVERT: F 47 TRP cc_start: 0.7471 (t60) cc_final: 0.6965 (t60) REVERT: F 80 TYR cc_start: 0.7509 (m-80) cc_final: 0.7187 (m-80) REVERT: H 111 GLN cc_start: 0.7910 (pm20) cc_final: 0.7554 (pm20) REVERT: L 3 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8061 (tm-30) outliers start: 14 outliers final: 12 residues processed: 152 average time/residue: 0.6056 time to fit residues: 123.1071 Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 6 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9774 Z= 0.208 Angle : 0.488 4.627 13263 Z= 0.255 Chirality : 0.046 0.157 1518 Planarity : 0.003 0.065 1692 Dihedral : 4.041 25.366 1329 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.42 % Allowed : 15.06 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.60 (0.25), residues: 1227 helix: 0.98 (0.67), residues: 75 sheet: -0.47 (0.23), residues: 540 loop : -0.36 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 90 HIS 0.004 0.001 HIS B 185 PHE 0.010 0.001 PHE A 207 TYR 0.010 0.001 TYR F 95 ARG 0.010 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7750 (t0) cc_final: 0.7462 (t0) REVERT: D 3 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8530 (mm110) REVERT: D 23 LYS cc_start: 0.8187 (tptt) cc_final: 0.7877 (tptm) REVERT: D 28 LYS cc_start: 0.6578 (ttpt) cc_final: 0.6233 (ttpt) REVERT: D 73 ASP cc_start: 0.5929 (t0) cc_final: 0.5551 (t0) REVERT: D 90 ASP cc_start: 0.7547 (t0) cc_final: 0.7165 (m-30) REVERT: E 77 LEU cc_start: 0.7784 (mt) cc_final: 0.7550 (mt) REVERT: F 47 TRP cc_start: 0.7470 (t60) cc_final: 0.6956 (t60) REVERT: F 80 TYR cc_start: 0.7428 (m-80) cc_final: 0.7117 (m-80) REVERT: H 111 GLN cc_start: 0.7956 (pm20) cc_final: 0.7580 (pm20) REVERT: L 3 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8084 (tm-30) outliers start: 15 outliers final: 15 residues processed: 152 average time/residue: 0.5756 time to fit residues: 115.7399 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 78 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9774 Z= 0.146 Angle : 0.467 4.496 13263 Z= 0.242 Chirality : 0.046 0.166 1518 Planarity : 0.003 0.043 1692 Dihedral : 3.836 24.205 1329 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.42 % Allowed : 15.15 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.44 (0.25), residues: 1227 helix: 1.21 (0.68), residues: 75 sheet: -0.40 (0.23), residues: 540 loop : -0.24 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 PHE 0.008 0.001 PHE L 82 TYR 0.007 0.001 TYR F 95 ARG 0.006 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7707 (t0) cc_final: 0.7414 (t0) REVERT: D 3 GLN cc_start: 0.8807 (mm-40) cc_final: 0.7895 (mp10) REVERT: D 23 LYS cc_start: 0.8163 (tptt) cc_final: 0.7913 (tptm) REVERT: D 28 LYS cc_start: 0.6533 (ttpt) cc_final: 0.6184 (ttpt) REVERT: D 46 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5390 (mt-10) REVERT: D 73 ASP cc_start: 0.6100 (t0) cc_final: 0.5711 (t0) REVERT: D 90 ASP cc_start: 0.7510 (t0) cc_final: 0.7150 (m-30) REVERT: D 103 ASP cc_start: 0.8152 (t0) cc_final: 0.7947 (m-30) REVERT: E 77 LEU cc_start: 0.7724 (mt) cc_final: 0.7459 (mt) REVERT: E 88 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6690 (tp-100) REVERT: F 47 TRP cc_start: 0.7506 (t60) cc_final: 0.6969 (t60) REVERT: F 80 TYR cc_start: 0.7413 (m-80) cc_final: 0.7093 (m-80) REVERT: G 4 MET cc_start: 0.8918 (mmp) cc_final: 0.8219 (mmp) REVERT: H 111 GLN cc_start: 0.7919 (pm20) cc_final: 0.7547 (pm20) outliers start: 15 outliers final: 13 residues processed: 148 average time/residue: 0.5568 time to fit residues: 110.7255 Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9774 Z= 0.264 Angle : 0.500 6.572 13263 Z= 0.261 Chirality : 0.046 0.159 1518 Planarity : 0.003 0.045 1692 Dihedral : 4.008 25.487 1329 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.61 % Allowed : 15.15 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.55 (0.25), residues: 1227 helix: 1.03 (0.67), residues: 75 sheet: -0.45 (0.23), residues: 540 loop : -0.33 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 109 HIS 0.004 0.001 HIS B 185 PHE 0.012 0.001 PHE A 207 TYR 0.011 0.001 TYR F 95 ARG 0.006 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7767 (t0) cc_final: 0.7469 (t0) REVERT: D 3 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8489 (mm110) REVERT: D 23 LYS cc_start: 0.8100 (tptt) cc_final: 0.7851 (tptm) REVERT: D 28 LYS cc_start: 0.6715 (ttpt) cc_final: 0.6384 (ttpt) REVERT: D 73 ASP cc_start: 0.5908 (t0) cc_final: 0.5570 (t0) REVERT: E 77 LEU cc_start: 0.7682 (mt) cc_final: 0.7427 (mt) REVERT: F 47 TRP cc_start: 0.7559 (t60) cc_final: 0.7065 (t60) REVERT: F 80 TYR cc_start: 0.7411 (m-80) cc_final: 0.7116 (m-80) REVERT: H 111 GLN cc_start: 0.7976 (pm20) cc_final: 0.7582 (pm20) outliers start: 17 outliers final: 16 residues processed: 150 average time/residue: 0.5809 time to fit residues: 115.7966 Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 73 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9774 Z= 0.174 Angle : 0.477 5.588 13263 Z= 0.246 Chirality : 0.045 0.160 1518 Planarity : 0.003 0.043 1692 Dihedral : 3.858 25.078 1329 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.14 % Allowed : 15.34 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.43 (0.25), residues: 1227 helix: 1.16 (0.68), residues: 75 sheet: -0.47 (0.23), residues: 495 loop : -0.17 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 PHE 0.008 0.001 PHE A 194 TYR 0.008 0.001 TYR F 95 ARG 0.006 0.000 ARG A 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7729 (t0) cc_final: 0.7426 (t0) REVERT: D 3 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8483 (mm110) REVERT: D 23 LYS cc_start: 0.8091 (tptt) cc_final: 0.7778 (tptm) REVERT: D 28 LYS cc_start: 0.6596 (ttpt) cc_final: 0.6258 (ttpt) REVERT: D 73 ASP cc_start: 0.6097 (t0) cc_final: 0.5775 (t0) REVERT: D 103 ASP cc_start: 0.8195 (t0) cc_final: 0.7978 (m-30) REVERT: F 80 TYR cc_start: 0.7383 (m-80) cc_final: 0.7098 (m-80) REVERT: G 4 MET cc_start: 0.8865 (mmp) cc_final: 0.8227 (mmp) REVERT: H 87 ARG cc_start: 0.5839 (mmm160) cc_final: 0.5628 (mmm160) REVERT: H 111 GLN cc_start: 0.7936 (pm20) cc_final: 0.7554 (pm20) outliers start: 12 outliers final: 12 residues processed: 148 average time/residue: 0.5748 time to fit residues: 113.2490 Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.174866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.122587 restraints weight = 42708.322| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.20 r_work: 0.3526 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9774 Z= 0.211 Angle : 0.490 6.044 13263 Z= 0.254 Chirality : 0.046 0.159 1518 Planarity : 0.003 0.042 1692 Dihedral : 3.909 25.439 1329 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.23 % Allowed : 15.53 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.49 (0.25), residues: 1227 helix: 1.11 (0.68), residues: 75 sheet: -0.34 (0.24), residues: 498 loop : -0.38 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 PHE 0.011 0.001 PHE A 207 TYR 0.009 0.001 TYR F 95 ARG 0.006 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4668.71 seconds wall clock time: 87 minutes 38.91 seconds (5258.91 seconds total)