Starting phenix.real_space_refine on Fri Nov 17 11:43:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/11_2023/7sjn_25162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/11_2023/7sjn_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_25162/11_2023/7sjn_25162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/11_2023/7sjn_25162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/11_2023/7sjn_25162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjn_25162/11_2023/7sjn_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 8.44, per 1000 atoms: 0.44 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: 13.54 Conformation dependent library (CDL) restraints added in 1.9 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: 1.66 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: 6.70 Time building geometry restraints manager: 14.13 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: 7070 17.28 - 34.57: 527 34.57 - 51.85: 72 51.85 - 69.13: 20 69.13 - 86.42: 9 Dihedral angle restraints: 7698 sinusoidal: 3531 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 7695 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 5.830 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 57.980 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.870 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.601 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 outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.5655 time to fit residues: 152.3298 Evaluate side-chains 142 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9065 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 94 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- 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: 0.7181 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9774 Z= 0.163 Angle : 0.499 4.465 13263 Z= 0.264 Chirality : 0.046 0.153 1518 Planarity : 0.003 0.040 1692 Dihedral : 3.842 15.835 1329 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.38 % Allowed : 8.05 % Favored : 91.57 % 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: -0.32 (0.25), residues: 1227 helix: 1.73 (0.72), residues: 66 sheet: -0.41 (0.23), residues: 516 loop : -0.10 (0.26), residues: 645 *********************** 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 168 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.627 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 outliers start: 4 outliers final: 3 residues processed: 164 average time/residue: 0.5786 time to fit residues: 125.5143 Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.461 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2013 time to fit residues: 3.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN D 111 GLN E 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9774 Z= 0.245 Angle : 0.518 7.226 13263 Z= 0.272 Chirality : 0.046 0.162 1518 Planarity : 0.003 0.029 1692 Dihedral : 3.974 19.268 1329 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.33 % Allowed : 9.19 % Favored : 89.49 % 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: -0.33 (0.25), residues: 1227 helix: 1.33 (0.69), residues: 72 sheet: -0.29 (0.23), residues: 519 loop : -0.20 (0.26), residues: 636 *********************** 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 167 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.357 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 outliers start: 14 outliers final: 13 residues processed: 159 average time/residue: 0.5539 time to fit residues: 117.7691 Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2213 time to fit residues: 7.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9774 Z= 0.203 Angle : 0.490 5.123 13263 Z= 0.256 Chirality : 0.046 0.158 1518 Planarity : 0.003 0.030 1692 Dihedral : 3.882 19.856 1329 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.09 % Allowed : 10.89 % Favored : 89.02 % 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: -0.30 (0.25), residues: 1227 helix: 1.38 (0.69), residues: 72 sheet: -0.27 (0.23), residues: 519 loop : -0.19 (0.26), residues: 636 *********************** 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 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.629 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 outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.5846 time to fit residues: 118.5982 Evaluate side-chains 138 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2055 time to fit residues: 2.3658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9774 Z= 0.246 Angle : 0.501 4.455 13263 Z= 0.263 Chirality : 0.046 0.160 1518 Planarity : 0.003 0.053 1692 Dihedral : 3.983 24.223 1329 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.95 % Allowed : 12.12 % Favored : 86.93 % 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: -0.37 (0.25), residues: 1227 helix: 1.24 (0.69), residues: 72 sheet: -0.31 (0.24), residues: 489 loop : -0.25 (0.25), residues: 666 *********************** 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 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.733 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 outliers start: 10 outliers final: 6 residues processed: 151 average time/residue: 0.5647 time to fit residues: 114.5652 Evaluate side-chains 143 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.547 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2367 time to fit residues: 4.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9774 Z= 0.167 Angle : 0.478 4.336 13263 Z= 0.248 Chirality : 0.046 0.156 1518 Planarity : 0.003 0.034 1692 Dihedral : 3.829 23.792 1329 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.38 % Allowed : 13.45 % Favored : 86.17 % 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: -0.21 (0.25), residues: 1227 helix: 1.39 (0.70), residues: 72 sheet: -0.16 (0.24), residues: 495 loop : -0.18 (0.25), residues: 660 *********************** 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 145 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.412 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 outliers start: 4 outliers final: 4 residues processed: 143 average time/residue: 0.5826 time to fit residues: 112.0316 Evaluate side-chains 139 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.480 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2257 time to fit residues: 3.5621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 0.0070 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9004 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9774 Z= 0.243 Angle : 0.503 4.464 13263 Z= 0.263 Chirality : 0.046 0.161 1518 Planarity : 0.003 0.034 1692 Dihedral : 3.964 25.236 1329 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.57 % Allowed : 13.73 % Favored : 85.70 % 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: -0.37 (0.25), residues: 1227 helix: 1.24 (0.69), residues: 72 sheet: -0.36 (0.24), residues: 477 loop : -0.22 (0.25), residues: 678 *********************** 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 146 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.700 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 outliers start: 6 outliers final: 5 residues processed: 142 average time/residue: 0.5904 time to fit residues: 110.5474 Evaluate side-chains 141 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.500 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2204 time to fit residues: 4.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9774 Z= 0.194 Angle : 0.490 4.426 13263 Z= 0.254 Chirality : 0.046 0.158 1518 Planarity : 0.003 0.044 1692 Dihedral : 3.884 24.750 1329 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.38 % Allowed : 14.39 % Favored : 85.23 % 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: -0.31 (0.25), residues: 1227 helix: 1.33 (0.69), residues: 72 sheet: -0.22 (0.23), residues: 513 loop : -0.25 (0.25), residues: 642 *********************** 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 142 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.439 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 outliers start: 4 outliers final: 3 residues processed: 141 average time/residue: 0.5744 time to fit residues: 107.7139 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.485 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2417 time to fit residues: 3.0831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9774 Z= 0.203 Angle : 0.500 5.635 13263 Z= 0.258 Chirality : 0.046 0.158 1518 Planarity : 0.003 0.039 1692 Dihedral : 3.871 24.395 1329 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.19 % Allowed : 14.68 % Favored : 85.13 % 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: 0.93 (0.67), residues: 78 sheet: -0.29 (0.24), residues: 489 loop : -0.25 (0.25), residues: 660 *********************** 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 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.530 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 outliers start: 2 outliers final: 2 residues processed: 135 average time/residue: 0.6014 time to fit residues: 107.6185 Evaluate side-chains 131 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.584 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3011 time to fit residues: 2.9081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 H 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9774 Z= 0.235 Angle : 0.514 6.347 13263 Z= 0.267 Chirality : 0.046 0.165 1518 Planarity : 0.003 0.040 1692 Dihedral : 3.955 24.544 1329 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.47 % Allowed : 14.77 % Favored : 84.75 % 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: -0.41 (0.25), residues: 1227 helix: 0.88 (0.67), residues: 78 sheet: -0.29 (0.24), residues: 489 loop : -0.29 (0.25), residues: 660 ********************** 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 140 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.524 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 outliers start: 5 outliers final: 5 residues processed: 138 average time/residue: 0.6028 time to fit residues: 108.9963 Evaluate side-chains 137 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.529 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2757 time to fit residues: 4.2214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.0010 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.177700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125332 restraints weight = 42777.559| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.21 r_work: 0.3559 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9774 Z= 0.147 Angle : 0.482 5.125 13263 Z= 0.248 Chirality : 0.046 0.155 1518 Planarity : 0.003 0.041 1692 Dihedral : 3.759 24.420 1329 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.09 % Allowed : 14.30 % Favored : 85.61 % 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: -0.28 (0.25), residues: 1227 helix: 1.06 (0.67), residues: 78 sheet: -0.29 (0.23), residues: 495 loop : -0.12 (0.25), residues: 654 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.33 seconds wall clock time: 83 minutes 46.98 seconds (5026.98 seconds total)