Starting phenix.real_space_refine on Fri Dec 8 06:10:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc6_34653/12_2023/8hc6_34653.pdb" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4704 2.51 5 N 1226 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2134 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1929 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.46, per 1000 atoms: 0.60 Number of scatterers: 7377 At special positions: 0 Unit cell: (112.2, 84.15, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1420 8.00 N 1226 7.00 C 4704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG C 601 " - " ASN C 331 " " NAG C 602 " - " ASN C 343 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 4.3% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.666A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.769A pdb=" N LEU C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.531A pdb=" N SER H 191 " --> pdb=" O PRO H 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 192 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'L' and resid 184 through 188 removed outlier: 4.126A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.619A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.667A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.538A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 77 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 123 through 126 removed outlier: 3.538A pdb=" N LYS H 146 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 123 through 126 removed outlier: 3.538A pdb=" N LYS H 146 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.755A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.790A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.548A pdb=" N VAL L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.949A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN L 38 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN L 90 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.761A pdb=" N PHE L 117 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU L 136 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 149 through 151 removed outlier: 4.273A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 192 through 193 removed outlier: 3.622A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.628A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.843A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 141 removed outlier: 4.519A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) 147 hydrogen bonds defined for protein. 375 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: 2.02 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2336 1.35 - 1.46: 1912 1.46 - 1.58: 3276 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 7555 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 7550 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.11: 231 107.11 - 113.85: 4161 113.85 - 120.58: 2696 120.58 - 127.32: 3107 127.32 - 134.05: 77 Bond angle restraints: 10272 Sorted by residual: angle pdb=" C ARG L 109 " pdb=" N THR L 110 " pdb=" CA THR L 110 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C SER H 206 " pdb=" N ASN H 207 " pdb=" CA ASN H 207 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.49e+00 angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 113.53 110.68 2.85 9.80e-01 1.04e+00 8.47e+00 angle pdb=" C GLY H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" N CYS H 219 " pdb=" CA CYS H 219 " pdb=" C CYS H 219 " ideal model delta sigma weight residual 114.04 110.59 3.45 1.24e+00 6.50e-01 7.75e+00 ... (remaining 10267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 4057 15.92 - 31.83: 407 31.83 - 47.75: 81 47.75 - 63.67: 16 63.67 - 79.58: 15 Dihedral angle restraints: 4576 sinusoidal: 1868 harmonic: 2708 Sorted by residual: dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual 93.00 168.38 -75.38 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.82 -48.82 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 138.26 -45.26 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 4573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1009 0.065 - 0.130: 150 0.130 - 0.196: 5 0.196 - 0.261: 2 0.261 - 0.326: 1 Chirality restraints: 1167 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1164 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 524 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C VAL C 524 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL C 524 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS C 525 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 235 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ILE B 235 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 235 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 236 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO C 330 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.019 5.00e-02 4.00e+02 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2188 2.82 - 3.34: 5884 3.34 - 3.86: 11654 3.86 - 4.38: 12475 4.38 - 4.90: 21939 Nonbonded interactions: 54140 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.296 2.440 nonbonded pdb=" O PRO H 126 " pdb=" OG SER L 122 " model vdw 2.339 2.440 nonbonded pdb=" OH TYR C 501 " pdb=" O GLY L 30 " model vdw 2.346 2.440 nonbonded pdb=" O LYS B 278 " pdb=" OG1 THR B 286 " model vdw 2.352 2.440 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR H 33 " model vdw 2.353 2.440 ... (remaining 54135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.230 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.003 0.043 7555 Z= 0.178 Angle : 0.566 7.001 10272 Z= 0.284 Chirality : 0.045 0.326 1167 Planarity : 0.004 0.034 1310 Dihedral : 13.451 79.582 2806 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 913 helix: -3.66 (0.60), residues: 24 sheet: 0.99 (0.34), residues: 235 loop : -1.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 32 HIS 0.003 0.000 HIS H 203 PHE 0.014 0.001 PHE L 140 TYR 0.008 0.001 TYR H 93 ARG 0.003 0.000 ARG L 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1896 time to fit residues: 16.5229 Evaluate side-chains 33 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7555 Z= 0.249 Angle : 0.593 7.379 10272 Z= 0.312 Chirality : 0.044 0.344 1167 Planarity : 0.004 0.032 1310 Dihedral : 5.107 48.915 1151 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 913 helix: -3.19 (0.60), residues: 26 sheet: 0.26 (0.35), residues: 240 loop : -0.88 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 35 HIS 0.005 0.002 HIS H 203 PHE 0.016 0.002 PHE B 220 TYR 0.014 0.002 TYR B 91 ARG 0.010 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1519 time to fit residues: 12.7438 Evaluate side-chains 26 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN H 35 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7555 Z= 0.176 Angle : 0.492 6.976 10272 Z= 0.254 Chirality : 0.043 0.320 1167 Planarity : 0.004 0.058 1310 Dihedral : 4.678 53.606 1151 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 913 helix: -2.58 (0.71), residues: 27 sheet: 0.37 (0.33), residues: 252 loop : -0.84 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.003 0.001 HIS H 203 PHE 0.010 0.001 PHE B 135 TYR 0.009 0.001 TYR H 33 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.829 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1478 time to fit residues: 12.2711 Evaluate side-chains 23 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 450 ASN H 35 HIS B 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7555 Z= 0.192 Angle : 0.512 8.327 10272 Z= 0.265 Chirality : 0.043 0.321 1167 Planarity : 0.004 0.046 1310 Dihedral : 4.551 49.238 1151 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 913 helix: -2.63 (0.69), residues: 30 sheet: 0.39 (0.34), residues: 240 loop : -0.97 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 436 HIS 0.005 0.001 HIS H 203 PHE 0.014 0.001 PHE C 375 TYR 0.015 0.001 TYR B 279 ARG 0.006 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1519 time to fit residues: 12.0911 Evaluate side-chains 24 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN C 450 ASN H 35 HIS H 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7555 Z= 0.165 Angle : 0.495 8.787 10272 Z= 0.255 Chirality : 0.043 0.311 1167 Planarity : 0.004 0.043 1310 Dihedral : 4.455 45.144 1151 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.27), residues: 913 helix: -2.58 (0.69), residues: 31 sheet: 0.28 (0.35), residues: 236 loop : -0.97 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS H 203 PHE 0.010 0.001 PHE B 238 TYR 0.009 0.001 TYR H 197 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1714 time to fit residues: 12.4507 Evaluate side-chains 29 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.0020 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7555 Z= 0.277 Angle : 0.618 11.202 10272 Z= 0.321 Chirality : 0.044 0.317 1167 Planarity : 0.004 0.042 1310 Dihedral : 5.123 46.841 1151 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 913 helix: -2.85 (0.69), residues: 36 sheet: -0.18 (0.32), residues: 262 loop : -1.07 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 258 HIS 0.022 0.003 HIS B 49 PHE 0.012 0.002 PHE B 65 TYR 0.014 0.002 TYR L 187 ARG 0.017 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1598 time to fit residues: 11.3944 Evaluate side-chains 22 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7555 Z= 0.180 Angle : 0.529 9.854 10272 Z= 0.273 Chirality : 0.043 0.317 1167 Planarity : 0.004 0.053 1310 Dihedral : 4.890 42.185 1151 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 913 helix: -2.90 (0.68), residues: 36 sheet: -0.14 (0.33), residues: 258 loop : -1.06 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 258 HIS 0.011 0.001 HIS B 49 PHE 0.009 0.001 PHE B 65 TYR 0.010 0.001 TYR L 141 ARG 0.007 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.899 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1666 time to fit residues: 11.6994 Evaluate side-chains 22 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.0060 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7555 Z= 0.144 Angle : 0.507 8.466 10272 Z= 0.261 Chirality : 0.044 0.315 1167 Planarity : 0.004 0.040 1310 Dihedral : 4.500 39.455 1151 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.28), residues: 913 helix: -3.07 (0.66), residues: 36 sheet: -0.07 (0.32), residues: 265 loop : -1.00 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 258 HIS 0.009 0.001 HIS B 49 PHE 0.012 0.001 PHE B 133 TYR 0.014 0.001 TYR C 369 ARG 0.007 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1581 time to fit residues: 12.0274 Evaluate side-chains 21 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 86 optimal weight: 0.0970 chunk 52 optimal weight: 0.0870 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7555 Z= 0.222 Angle : 0.563 9.232 10272 Z= 0.293 Chirality : 0.044 0.312 1167 Planarity : 0.004 0.042 1310 Dihedral : 4.753 40.307 1151 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 913 helix: -3.10 (0.65), residues: 38 sheet: -0.12 (0.32), residues: 257 loop : -1.10 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 258 HIS 0.018 0.002 HIS B 49 PHE 0.013 0.002 PHE B 65 TYR 0.013 0.002 TYR C 369 ARG 0.007 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.813 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1634 time to fit residues: 11.5931 Evaluate side-chains 22 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN B 185 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7555 Z= 0.196 Angle : 0.533 8.812 10272 Z= 0.277 Chirality : 0.044 0.314 1167 Planarity : 0.004 0.040 1310 Dihedral : 4.752 40.571 1151 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 913 helix: -3.05 (0.64), residues: 38 sheet: -0.16 (0.32), residues: 263 loop : -1.04 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 258 HIS 0.017 0.002 HIS B 49 PHE 0.011 0.001 PHE B 43 TYR 0.011 0.001 TYR B 279 ARG 0.008 0.001 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.881 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1471 time to fit residues: 10.9259 Evaluate side-chains 24 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.0030 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.073809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055236 restraints weight = 46342.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056508 restraints weight = 31042.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057354 restraints weight = 18927.632| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7555 Z= 0.143 Angle : 0.504 7.596 10272 Z= 0.259 Chirality : 0.043 0.316 1167 Planarity : 0.004 0.039 1310 Dihedral : 4.531 38.168 1151 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 913 helix: -3.12 (0.60), residues: 38 sheet: -0.17 (0.32), residues: 259 loop : -0.91 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 258 HIS 0.013 0.001 HIS B 49 PHE 0.009 0.001 PHE B 238 TYR 0.008 0.001 TYR C 380 ARG 0.005 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.27 seconds wall clock time: 27 minutes 27.68 seconds (1647.68 seconds total)