Starting phenix.real_space_refine on Thu Oct 10 10:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y52_38928/10_2024/8y52_38928.cif" } resolution = 2.9 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= -0.000 sd= 0.057 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 45 5.16 5 C 4706 2.51 5 N 1272 2.21 5 O 1357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 7380 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2392 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "X" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'BAL': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.69 Number of scatterers: 7380 At special positions: 0 Unit cell: (88.4, 82.16, 134.16, 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 45 16.00 O 1357 8.00 N 1272 7.00 C 4706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 203 " distance=2.03 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN X 1 " Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 46.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.606A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.591A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.556A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.531A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.523A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 50 through 75 Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 82 through 108 removed outlier: 3.608A pdb=" N ILE R 86 " --> pdb=" O PRO R 82 " (cutoff:3.500A) Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.629A pdb=" N ARG R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 186 removed outlier: 3.668A pdb=" N THR R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Proline residue: R 181 - end of helix Processing helix chain 'R' and resid 207 through 209 No H-bonds generated for 'chain 'R' and resid 207 through 209' Processing helix chain 'R' and resid 210 through 226 Processing helix chain 'R' and resid 226 through 251 Processing helix chain 'R' and resid 259 through 298 removed outlier: 3.634A pdb=" N VAL R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 307 through 334 removed outlier: 4.045A pdb=" N PHE R 311 " --> pdb=" O MET R 307 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER R 323 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Proline residue: R 327 - end of helix removed outlier: 3.506A pdb=" N SER R 334 " --> pdb=" O LEU R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.518A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.243A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.514A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.682A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 119 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.665A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 166 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.104A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.168A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.755A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 187 through 193 removed outlier: 3.570A pdb=" N MET R 198 " --> pdb=" O ASP R 193 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1158 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: 2.09 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1194 1.29 - 1.42: 1976 1.42 - 1.55: 4296 1.55 - 1.68: 2 1.68 - 1.81: 62 Bond restraints: 7530 Sorted by residual: bond pdb=" C BAL X 6 " pdb=" N HIS X 7 " ideal model delta sigma weight residual 1.343 1.500 -0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" C VAL X 5 " pdb=" N BAL X 6 " ideal model delta sigma weight residual 1.334 1.268 0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" CA BAL X 6 " pdb=" CB BAL X 6 " ideal model delta sigma weight residual 1.521 1.371 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" C VAL X 5 " pdb=" O VAL X 5 " ideal model delta sigma weight residual 1.231 1.154 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" N BAL X 6 " pdb=" CB BAL X 6 " ideal model delta sigma weight residual 1.458 1.416 0.042 2.00e-02 2.50e+03 4.39e+00 ... (remaining 7525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 10192 5.85 - 11.70: 3 11.70 - 17.55: 1 17.55 - 23.40: 2 23.40 - 29.25: 1 Bond angle restraints: 10199 Sorted by residual: angle pdb=" C BAL X 6 " pdb=" CA BAL X 6 " pdb=" CB BAL X 6 " ideal model delta sigma weight residual 110.50 139.75 -29.25 1.50e+00 4.44e-01 3.80e+02 angle pdb=" CA BAL X 6 " pdb=" C BAL X 6 " pdb=" N HIS X 7 " ideal model delta sigma weight residual 115.94 93.57 22.36 2.00e+00 2.50e-01 1.25e+02 angle pdb=" C BAL X 6 " pdb=" N HIS X 7 " pdb=" CA HIS X 7 " ideal model delta sigma weight residual 120.82 102.16 18.66 1.80e+00 3.09e-01 1.07e+02 angle pdb=" CA BAL X 6 " pdb=" C BAL X 6 " pdb=" O BAL X 6 " ideal model delta sigma weight residual 120.80 135.52 -14.72 1.70e+00 3.46e-01 7.49e+01 angle pdb=" O BAL X 6 " pdb=" C BAL X 6 " pdb=" N HIS X 7 " ideal model delta sigma weight residual 121.31 130.05 -8.74 1.60e+00 3.91e-01 2.98e+01 ... (remaining 10194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.63: 4416 18.63 - 37.26: 75 37.26 - 55.90: 11 55.90 - 74.53: 4 74.53 - 93.16: 3 Dihedral angle restraints: 4509 sinusoidal: 1777 harmonic: 2732 Sorted by residual: dihedral pdb=" N BAL X 6 " pdb=" C BAL X 6 " pdb=" CA BAL X 6 " pdb=" CB BAL X 6 " ideal model delta harmonic sigma weight residual 122.80 29.64 93.16 0 2.50e+00 1.60e-01 1.39e+03 dihedral pdb=" C BAL X 6 " pdb=" N BAL X 6 " pdb=" CA BAL X 6 " pdb=" CB BAL X 6 " ideal model delta harmonic sigma weight residual -122.60 -33.78 -88.82 0 2.50e+00 1.60e-01 1.26e+03 dihedral pdb=" CB CYS R 120 " pdb=" SG CYS R 120 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 144.41 -51.41 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 4506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1033 0.060 - 0.120: 127 0.120 - 0.179: 8 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 1169 Sorted by residual: chirality pdb=" CA HIS X 7 " pdb=" N HIS X 7 " pdb=" C HIS X 7 " pdb=" CB HIS X 7 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE R 251 " pdb=" N ILE R 251 " pdb=" C ILE R 251 " pdb=" CB ILE R 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1166 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BAL X 6 " -0.014 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C BAL X 6 " 0.051 2.00e-02 2.50e+03 pdb=" O BAL X 6 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS X 7 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL X 5 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C VAL X 5 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL X 5 " -0.019 2.00e-02 2.50e+03 pdb=" N BAL X 6 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 3 " 0.022 2.00e-02 2.50e+03 1.09e-02 2.96e+00 pdb=" CG TRP X 3 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP X 3 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP X 3 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP X 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP X 3 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP X 3 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 3 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 3 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 3 " 0.004 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 103 2.62 - 3.19: 7105 3.19 - 3.76: 11405 3.76 - 4.33: 15922 4.33 - 4.90: 26608 Nonbonded interactions: 61143 Sorted by model distance: nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.056 3.040 nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 141 " model vdw 2.096 3.040 nonbonded pdb=" OD2 ASP B 210 " pdb=" OG SER B 212 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASN A 216 " pdb=" NZ LYS B 62 " model vdw 2.155 3.120 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.164 3.040 ... (remaining 61138 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.950 Find NCS groups from input model: 0.100 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 7530 Z= 0.311 Angle : 0.622 29.248 10199 Z= 0.363 Chirality : 0.038 0.299 1169 Planarity : 0.003 0.031 1288 Dihedral : 7.692 82.149 2730 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.25 % Allowed : 2.60 % Favored : 97.15 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 915 helix: 0.11 (0.25), residues: 405 sheet: -1.93 (0.33), residues: 200 loop : -1.63 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 3 HIS 0.005 0.001 HIS R 340 PHE 0.006 0.001 PHE A 189 TYR 0.004 0.000 TYR R 237 ARG 0.002 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASP cc_start: 0.5409 (t0) cc_final: 0.4845 (t0) REVERT: G 49 LEU cc_start: 0.6152 (mp) cc_final: 0.5659 (mp) REVERT: R 104 ASP cc_start: 0.5609 (m-30) cc_final: 0.5154 (m-30) REVERT: R 258 HIS cc_start: 0.4225 (t70) cc_final: 0.3915 (t70) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 1.2735 time to fit residues: 294.8615 Evaluate side-chains 105 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN R 258 HIS R 322 ASN X 2 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.375 7530 Z= 0.678 Angle : 0.963 22.554 10199 Z= 0.502 Chirality : 0.050 0.445 1169 Planarity : 0.006 0.077 1288 Dihedral : 3.804 51.628 1020 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.35 % Allowed : 16.98 % Favored : 79.68 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 915 helix: 0.48 (0.25), residues: 407 sheet: -1.70 (0.33), residues: 202 loop : -1.46 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 87 HIS 0.009 0.001 HIS R 308 PHE 0.021 0.002 PHE A 343 TYR 0.011 0.002 TYR R 54 ARG 0.015 0.001 ARG G 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6425 (mpp80) REVERT: B 222 MET cc_start: 0.6720 (ppp) cc_final: 0.4980 (ppp) REVERT: B 280 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8325 (p) outliers start: 27 outliers final: 10 residues processed: 125 average time/residue: 1.2673 time to fit residues: 167.7112 Evaluate side-chains 104 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 308 HIS Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.375 7530 Z= 0.678 Angle : 0.963 22.554 10199 Z= 0.502 Chirality : 0.050 0.445 1169 Planarity : 0.006 0.077 1288 Dihedral : 3.716 51.628 1018 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 40.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.49 % Allowed : 21.44 % Favored : 77.08 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 915 helix: 0.48 (0.25), residues: 407 sheet: -1.70 (0.33), residues: 202 loop : -1.46 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 87 HIS 0.009 0.001 HIS R 308 PHE 0.021 0.002 PHE A 343 TYR 0.011 0.002 TYR R 54 ARG 0.015 0.001 ARG G 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 1.1914 time to fit residues: 126.7974 Evaluate side-chains 98 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 308 HIS Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.229 7530 Z= 0.550 Angle : 0.984 23.118 10199 Z= 0.505 Chirality : 0.047 0.255 1169 Planarity : 0.008 0.178 1288 Dihedral : 3.912 48.581 1018 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 19.33 % Favored : 77.57 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.27), residues: 915 helix: 0.66 (0.25), residues: 408 sheet: -1.48 (0.34), residues: 198 loop : -1.46 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 87 HIS 0.010 0.002 HIS R 308 PHE 0.021 0.002 PHE R 296 TYR 0.012 0.001 TYR R 54 ARG 0.021 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 1.2991 time to fit residues: 148.4716 Evaluate side-chains 98 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 7530 Z= 0.550 Angle : 0.984 23.118 10199 Z= 0.505 Chirality : 0.047 0.255 1169 Planarity : 0.008 0.178 1288 Dihedral : 3.912 48.581 1018 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 31.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 21.93 % Favored : 76.58 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.27), residues: 915 helix: 0.66 (0.25), residues: 408 sheet: -1.48 (0.34), residues: 198 loop : -1.46 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 87 HIS 0.010 0.002 HIS R 308 PHE 0.021 0.002 PHE R 296 TYR 0.012 0.001 TYR R 54 ARG 0.021 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 13 residues processed: 94 average time/residue: 1.1689 time to fit residues: 116.8459 Evaluate side-chains 96 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 7530 Z= 0.550 Angle : 0.984 23.118 10199 Z= 0.505 Chirality : 0.047 0.255 1169 Planarity : 0.008 0.178 1288 Dihedral : 3.912 48.581 1018 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 33.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.61 % Allowed : 22.18 % Favored : 76.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.27), residues: 915 helix: 0.66 (0.25), residues: 408 sheet: -1.48 (0.34), residues: 198 loop : -1.46 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 87 HIS 0.010 0.002 HIS R 308 PHE 0.021 0.002 PHE R 296 TYR 0.012 0.001 TYR R 54 ARG 0.021 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 92 average time/residue: 1.1909 time to fit residues: 116.6732 Evaluate side-chains 96 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 7530 Z= 0.552 Angle : 0.979 24.046 10199 Z= 0.502 Chirality : 0.048 0.249 1169 Planarity : 0.007 0.121 1288 Dihedral : 4.058 57.301 1018 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.35 % Allowed : 20.94 % Favored : 76.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.27), residues: 915 helix: 0.77 (0.25), residues: 408 sheet: -1.41 (0.33), residues: 203 loop : -1.45 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.011 0.002 HIS R 308 PHE 0.015 0.002 PHE R 296 TYR 0.015 0.002 TYR A 358 ARG 0.014 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 1.2653 time to fit residues: 135.9685 Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 7530 Z= 0.552 Angle : 0.979 24.046 10199 Z= 0.502 Chirality : 0.048 0.249 1169 Planarity : 0.007 0.121 1288 Dihedral : 4.058 57.301 1018 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 22.30 % Favored : 75.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.27), residues: 915 helix: 0.77 (0.25), residues: 408 sheet: -1.41 (0.33), residues: 203 loop : -1.45 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.011 0.002 HIS R 308 PHE 0.015 0.002 PHE R 296 TYR 0.015 0.002 TYR A 358 ARG 0.014 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 89 average time/residue: 1.1883 time to fit residues: 112.8074 Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 7530 Z= 0.552 Angle : 0.979 24.046 10199 Z= 0.502 Chirality : 0.048 0.249 1169 Planarity : 0.007 0.121 1288 Dihedral : 4.058 57.301 1018 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 22.30 % Favored : 75.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.27), residues: 915 helix: 0.77 (0.25), residues: 408 sheet: -1.41 (0.33), residues: 203 loop : -1.45 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.011 0.002 HIS R 308 PHE 0.015 0.002 PHE R 296 TYR 0.015 0.002 TYR A 358 ARG 0.014 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 89 average time/residue: 1.1921 time to fit residues: 113.1017 Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 7530 Z= 0.552 Angle : 0.979 24.045 10199 Z= 0.502 Chirality : 0.048 0.249 1169 Planarity : 0.007 0.121 1288 Dihedral : 4.058 57.301 1018 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.73 % Allowed : 22.43 % Favored : 75.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.27), residues: 915 helix: 0.77 (0.25), residues: 408 sheet: -1.41 (0.33), residues: 203 loop : -1.45 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.011 0.002 HIS R 308 PHE 0.015 0.002 PHE R 296 TYR 0.015 0.002 TYR A 358 ARG 0.014 0.001 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 15 residues processed: 89 average time/residue: 1.2157 time to fit residues: 115.0964 Evaluate side-chains 95 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 312 THR Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.070832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055912 restraints weight = 29739.032| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.01 r_work: 0.3048 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 7530 Z= 0.552 Angle : 0.979 24.045 10199 Z= 0.502 Chirality : 0.048 0.249 1169 Planarity : 0.007 0.121 1288 Dihedral : 4.058 57.301 1018 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 22.30 % Favored : 75.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.27), residues: 915 helix: 0.77 (0.25), residues: 408 sheet: -1.41 (0.33), residues: 203 loop : -1.45 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.011 0.002 HIS R 308 PHE 0.015 0.002 PHE R 296 TYR 0.015 0.002 TYR A 358 ARG 0.014 0.001 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.78 seconds wall clock time: 53 minutes 7.25 seconds (3187.25 seconds total)