Starting phenix.real_space_refine on Mon Sep 30 08:24:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljo_4061/09_2024/5ljo_4061.cif" } resolution = 4.9 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= 0.008 sd= 0.058 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 33 5.16 5 C 7986 2.51 5 N 2172 2.21 5 O 2501 1.98 5 H 12255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24947 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2498 Classifications: {'peptide': 165} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 153} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1352 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A" Number of atoms: 12102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 12102 Classifications: {'peptide': 783} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 751} Time building chain proxies: 11.79, per 1000 atoms: 0.47 Number of scatterers: 24947 At special positions: 0 Unit cell: (137.28, 115.44, 138.32, 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 33 16.00 O 2501 8.00 N 2172 7.00 C 7986 6.00 H 12255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2972 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 20 sheets defined 24.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 removed outlier: 4.728A pdb=" N ALA E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.081A pdb=" N VAL A 208 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.356A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.604A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.121A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.272A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.032A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 7.100A pdb=" N SER B 193 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 255 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.495A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.372A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.500A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.497A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.067A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 161 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP C 144 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 163 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR C 142 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 165 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR C 140 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.440A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 73 through 79 removed outlier: 5.982A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AB6, first strand: chain 'A' and resid 94 through 100 removed outlier: 4.626A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 171 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER A 148 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 174 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 146 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 294 through 295 removed outlier: 5.684A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 349 through 355 removed outlier: 4.739A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.409A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.564A pdb=" N SER A 472 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 494 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.189A pdb=" N GLY A 662 " --> pdb=" O GLU A 800 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1542 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: 9.87 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 12252 1.12 - 1.29: 2199 1.29 - 1.47: 5190 1.47 - 1.64: 5516 1.64 - 1.81: 63 Bond restraints: 25220 Sorted by residual: bond pdb=" CE1 TYR A 688 " pdb=" HE1 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" CD2 TYR A 688 " pdb=" HD2 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" CD1 TYR A 688 " pdb=" HD1 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" CE2 TYR A 688 " pdb=" HE2 TYR A 688 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N GLU A 645 " pdb=" H GLU A 645 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.57e+01 ... (remaining 25215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 40323 2.84 - 5.68: 3983 5.68 - 8.52: 1005 8.52 - 11.37: 43 11.37 - 14.21: 8 Bond angle restraints: 45362 Sorted by residual: angle pdb=" CA PHE A 395 " pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 113.80 104.92 8.88 1.00e+00 1.00e+00 7.88e+01 angle pdb=" C TYR D 62 " pdb=" N PRO D 63 " pdb=" CA PRO D 63 " ideal model delta sigma weight residual 119.56 128.48 -8.92 1.02e+00 9.61e-01 7.65e+01 angle pdb=" C ASP A 762 " pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 119.82 128.29 -8.47 9.80e-01 1.04e+00 7.47e+01 angle pdb=" C ALA C 45 " pdb=" N PRO C 46 " pdb=" CA PRO C 46 " ideal model delta sigma weight residual 120.03 128.51 -8.48 9.90e-01 1.02e+00 7.34e+01 angle pdb=" C GLY A 781 " pdb=" N PRO A 782 " pdb=" CA PRO A 782 " ideal model delta sigma weight residual 119.98 129.87 -9.89 1.16e+00 7.43e-01 7.26e+01 ... (remaining 45357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11310 17.65 - 35.31: 417 35.31 - 52.96: 159 52.96 - 70.62: 55 70.62 - 88.27: 16 Dihedral angle restraints: 11957 sinusoidal: 6453 harmonic: 5504 Sorted by residual: dihedral pdb=" CA ASP B 353 " pdb=" C ASP B 353 " pdb=" N GLY B 354 " pdb=" CA GLY B 354 " ideal model delta harmonic sigma weight residual 0.00 41.47 -41.47 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N THR A 93 " pdb=" CA THR A 93 " ideal model delta harmonic sigma weight residual 0.00 -37.88 37.88 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N GLY B 55 " pdb=" CA GLY B 55 " ideal model delta harmonic sigma weight residual 0.00 -37.30 37.30 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 11954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1229 0.069 - 0.137: 556 0.137 - 0.206: 125 0.206 - 0.275: 10 0.275 - 0.343: 9 Chirality restraints: 1929 Sorted by residual: chirality pdb=" CA PHE D 169 " pdb=" N PHE D 169 " pdb=" C PHE D 169 " pdb=" CB PHE D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PHE A 738 " pdb=" N PHE A 738 " pdb=" C PHE A 738 " pdb=" CB PHE A 738 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ARG A 162 " pdb=" N ARG A 162 " pdb=" C ARG A 162 " pdb=" CB ARG A 162 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1926 not shown) Planarity restraints: 3878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 533 " -0.105 2.00e-02 2.50e+03 1.11e-01 2.78e+02 pdb=" CG HIS A 533 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 533 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 HIS A 533 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS A 533 " -0.056 2.00e-02 2.50e+03 pdb=" NE2 HIS A 533 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 HIS A 533 " 0.259 2.00e-02 2.50e+03 pdb=" HD2 HIS A 533 " 0.091 2.00e-02 2.50e+03 pdb=" HE1 HIS A 533 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 625 " -0.082 2.00e-02 2.50e+03 8.70e-02 1.70e+02 pdb=" CG HIS A 625 " -0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS A 625 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 HIS A 625 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 625 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 625 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS A 625 " 0.202 2.00e-02 2.50e+03 pdb=" HD2 HIS A 625 " 0.069 2.00e-02 2.50e+03 pdb=" HE1 HIS A 625 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 92 " -0.063 2.00e-02 2.50e+03 1.28e-01 1.65e+02 pdb=" C PRO A 92 " 0.222 2.00e-02 2.50e+03 pdb=" O PRO A 92 " -0.082 2.00e-02 2.50e+03 pdb=" N THR A 93 " -0.076 2.00e-02 2.50e+03 ... (remaining 3875 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1945 2.08 - 2.71: 40470 2.71 - 3.34: 77908 3.34 - 3.97: 104516 3.97 - 4.60: 155602 Nonbonded interactions: 380441 Sorted by model distance: nonbonded pdb=" OE1 GLN D 69 " pdb=" H GLN D 69 " model vdw 1.449 2.450 nonbonded pdb=" OE1 GLN A 217 " pdb=" H GLN A 217 " model vdw 1.455 2.450 nonbonded pdb=" OE1 GLU A 420 " pdb=" H GLU A 420 " model vdw 1.486 2.450 nonbonded pdb=" O THR B 50 " pdb="HG23 THR B 50 " model vdw 1.499 2.620 nonbonded pdb=" H ARG A 661 " pdb=" HD2 ARG A 661 " model vdw 1.561 2.270 ... (remaining 380436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 9.520 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: 1.600 Extract box with map and model: 0.000 Check model and map are aligned: 0.160 Set scattering table: 0.160 Process input model: 53.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 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 : 0.014 0.071 12965 Z= 0.919 Angle : 1.687 11.523 17629 Z= 1.133 Chirality : 0.077 0.343 1929 Planarity : 0.013 0.132 2326 Dihedral : 11.005 88.270 4697 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 3.84 % Allowed : 9.36 % Favored : 86.80 % Rotamer: Outliers : 0.15 % Allowed : 0.59 % Favored : 99.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.19), residues: 1614 helix: -0.21 (0.23), residues: 348 sheet: -1.84 (0.24), residues: 404 loop : -2.24 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP E 73 HIS 0.009 0.002 HIS A 677 PHE 0.058 0.005 PHE A 395 TYR 0.064 0.008 TYR D 205 ARG 0.009 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.831 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: 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: E 90 THR cc_start: 0.6253 (m) cc_final: 0.5950 (m) REVERT: A 539 MET cc_start: 0.6928 (mpp) cc_final: 0.5961 (mpp) outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.6247 time to fit residues: 108.2033 Evaluate side-chains 87 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 302 ASN E 52 GLN A 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12965 Z= 0.350 Angle : 0.794 8.340 17629 Z= 0.451 Chirality : 0.046 0.178 1929 Planarity : 0.007 0.126 2326 Dihedral : 6.109 31.329 1781 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.54 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1614 helix: 0.01 (0.25), residues: 359 sheet: -1.90 (0.24), residues: 421 loop : -2.16 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 546 HIS 0.010 0.003 HIS E 83 PHE 0.030 0.003 PHE A 395 TYR 0.029 0.002 TYR A 686 ARG 0.007 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.075 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: 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: A 539 MET cc_start: 0.7678 (mpp) cc_final: 0.6755 (mpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.6785 time to fit residues: 100.3586 Evaluate side-chains 85 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12965 Z= 0.218 Angle : 0.633 8.618 17629 Z= 0.354 Chirality : 0.043 0.151 1929 Planarity : 0.005 0.129 2326 Dihedral : 5.778 34.485 1781 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.78 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.20), residues: 1614 helix: 0.30 (0.25), residues: 367 sheet: -1.95 (0.25), residues: 418 loop : -2.19 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.005 0.002 HIS E 83 PHE 0.029 0.002 PHE A 395 TYR 0.016 0.002 TYR B 263 ARG 0.006 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.015 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: 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 613 LEU cc_start: 0.7275 (tt) cc_final: 0.6798 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.6386 time to fit residues: 89.6366 Evaluate side-chains 80 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 463 ASN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 12965 Z= 0.434 Angle : 0.778 8.496 17629 Z= 0.444 Chirality : 0.043 0.158 1929 Planarity : 0.007 0.119 2326 Dihedral : 6.204 34.777 1781 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.07 % Favored : 86.31 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1614 helix: -0.42 (0.24), residues: 365 sheet: -1.93 (0.26), residues: 382 loop : -2.59 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 635 HIS 0.007 0.002 HIS A 186 PHE 0.031 0.003 PHE A 395 TYR 0.022 0.003 TYR A 686 ARG 0.010 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.975 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: 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: 0 residues processed: 81 average time/residue: 0.6473 time to fit residues: 74.4040 Evaluate side-chains 69 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12965 Z= 0.294 Angle : 0.667 6.899 17629 Z= 0.376 Chirality : 0.042 0.148 1929 Planarity : 0.006 0.113 2326 Dihedral : 6.102 34.843 1781 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.20 % Favored : 86.18 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.19), residues: 1614 helix: -0.30 (0.24), residues: 372 sheet: -2.17 (0.25), residues: 401 loop : -2.60 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 635 HIS 0.008 0.002 HIS A 625 PHE 0.026 0.002 PHE A 395 TYR 0.019 0.002 TYR A 266 ARG 0.009 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.989 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: 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 218 MET cc_start: 0.8157 (ttt) cc_final: 0.7369 (tpp) REVERT: A 226 LEU cc_start: 0.9581 (tp) cc_final: 0.9372 (tp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.6418 time to fit residues: 72.9167 Evaluate side-chains 71 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12965 Z= 0.230 Angle : 0.610 6.938 17629 Z= 0.340 Chirality : 0.042 0.165 1929 Planarity : 0.006 0.109 2326 Dihedral : 5.910 33.946 1781 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.64 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1614 helix: 0.13 (0.25), residues: 367 sheet: -2.18 (0.24), residues: 407 loop : -2.53 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 776 HIS 0.005 0.002 HIS B 347 PHE 0.021 0.002 PHE A 395 TYR 0.028 0.002 TYR A 255 ARG 0.007 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.205 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: 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 218 MET cc_start: 0.8155 (ttt) cc_final: 0.7373 (tpp) REVERT: A 226 LEU cc_start: 0.9578 (tp) cc_final: 0.9357 (tp) REVERT: A 613 LEU cc_start: 0.7508 (tt) cc_final: 0.7094 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.6226 time to fit residues: 70.6182 Evaluate side-chains 73 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12965 Z= 0.261 Angle : 0.623 6.828 17629 Z= 0.348 Chirality : 0.042 0.165 1929 Planarity : 0.005 0.108 2326 Dihedral : 5.911 33.874 1781 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.07 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.20), residues: 1614 helix: 0.15 (0.25), residues: 367 sheet: -2.20 (0.24), residues: 403 loop : -2.59 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 776 HIS 0.005 0.002 HIS B 347 PHE 0.022 0.002 PHE A 395 TYR 0.015 0.002 TYR B 263 ARG 0.008 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.113 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: 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 218 MET cc_start: 0.8158 (ttt) cc_final: 0.7432 (tpp) REVERT: A 226 LEU cc_start: 0.9606 (tp) cc_final: 0.9385 (tp) REVERT: A 613 LEU cc_start: 0.7523 (tt) cc_final: 0.7079 (tt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6222 time to fit residues: 69.9749 Evaluate side-chains 75 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12965 Z= 0.383 Angle : 0.736 6.444 17629 Z= 0.417 Chirality : 0.043 0.166 1929 Planarity : 0.007 0.106 2326 Dihedral : 6.337 33.886 1781 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.12 % Favored : 84.32 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.24 (0.19), residues: 1614 helix: -0.40 (0.25), residues: 365 sheet: -2.47 (0.24), residues: 404 loop : -2.84 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 635 HIS 0.009 0.003 HIS A 186 PHE 0.025 0.003 PHE A 478 TYR 0.026 0.003 TYR A 214 ARG 0.011 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.136 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 218 MET cc_start: 0.8078 (ttt) cc_final: 0.7455 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.6280 time to fit residues: 67.0964 Evaluate side-chains 71 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 50.0000 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12965 Z= 0.195 Angle : 0.605 6.494 17629 Z= 0.333 Chirality : 0.043 0.167 1929 Planarity : 0.006 0.104 2326 Dihedral : 5.971 32.453 1781 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.08 % Favored : 87.42 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1614 helix: 0.23 (0.26), residues: 366 sheet: -2.33 (0.24), residues: 408 loop : -2.65 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 776 HIS 0.006 0.001 HIS B 347 PHE 0.038 0.002 PHE A 804 TYR 0.022 0.002 TYR A 266 ARG 0.014 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.129 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 218 MET cc_start: 0.8102 (ttt) cc_final: 0.7460 (tpp) REVERT: A 226 LEU cc_start: 0.9582 (tp) cc_final: 0.9345 (tp) REVERT: A 613 LEU cc_start: 0.7375 (tt) cc_final: 0.6976 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.6142 time to fit residues: 69.8425 Evaluate side-chains 72 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.1980 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12965 Z= 0.250 Angle : 0.619 7.770 17629 Z= 0.344 Chirality : 0.042 0.149 1929 Planarity : 0.006 0.105 2326 Dihedral : 5.991 32.429 1781 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.51 % Favored : 86.00 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.20), residues: 1614 helix: 0.23 (0.26), residues: 364 sheet: -2.38 (0.24), residues: 401 loop : -2.71 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 776 HIS 0.006 0.002 HIS A 186 PHE 0.019 0.002 PHE A 785 TYR 0.016 0.002 TYR A 266 ARG 0.009 0.001 ARG A 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.214 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: 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 218 MET cc_start: 0.8112 (ttt) cc_final: 0.7539 (tpp) REVERT: A 226 LEU cc_start: 0.9586 (tp) cc_final: 0.9355 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.5974 time to fit residues: 65.1569 Evaluate side-chains 71 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 117 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.033665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023816 restraints weight = 542544.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.024862 restraints weight = 321188.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.025582 restraints weight = 215147.869| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12965 Z= 0.201 Angle : 0.585 8.526 17629 Z= 0.322 Chirality : 0.042 0.153 1929 Planarity : 0.005 0.109 2326 Dihedral : 5.856 32.337 1781 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.70 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.20), residues: 1614 helix: 0.45 (0.26), residues: 361 sheet: -2.33 (0.24), residues: 402 loop : -2.66 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 PHE 0.017 0.002 PHE A 785 TYR 0.016 0.002 TYR A 266 ARG 0.010 0.001 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.96 seconds wall clock time: 74 minutes 10.40 seconds (4450.40 seconds total)