Starting phenix.real_space_refine on Sat Feb 17 08:35:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/02_2024/8g02_29642.pdb" } resolution = 3.5 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5906 2.51 5 N 1480 2.21 5 O 1536 1.98 5 H 9228 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "H ASP 19": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18194 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345} Chain: "E" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 345} Chain: "B" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 59} Chain: "G" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Time building chain proxies: 8.21, per 1000 atoms: 0.45 Number of scatterers: 18194 At special positions: 0 Unit cell: (89.024, 103.168, 119.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1536 8.00 N 1480 7.00 C 5906 6.00 H 9228 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 62.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.434A pdb=" N LYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 53 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 75 through 91 removed outlier: 4.195A pdb=" N ILE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.665A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.881A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 220 removed outlier: 3.653A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.629A pdb=" N LEU A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.706A pdb=" N GLY A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 334 through 360 removed outlier: 3.764A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 41 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.566A pdb=" N LEU E 51 " --> pdb=" O HIS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.047A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.737A pdb=" N TRP E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 115 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.738A pdb=" N GLY E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU E 128 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.864A pdb=" N LYS E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 174 through 195 removed outlier: 3.798A pdb=" N LEU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 220 Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.776A pdb=" N PHE E 256 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.731A pdb=" N GLY E 269 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.534A pdb=" N HIS E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 removed outlier: 3.812A pdb=" N LEU E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.511A pdb=" N THR B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Proline residue: B 21 - end of helix removed outlier: 3.842A pdb=" N ILE B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.056A pdb=" N ARG B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.541A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 25 Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 51 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 143 through 149 Processing helix chain 'H' and resid 42 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 143 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.756A pdb=" N THR F 110 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL F 118 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL F 112 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.825A pdb=" N LYS G 57 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 118 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL H 112 " --> pdb=" O HIS H 116 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 138 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 12 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL F 136 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN F 14 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL F 134 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG F 16 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE F 132 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL H 8 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE H 139 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER H 10 " --> pdb=" O VAL H 137 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 16.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9222 1.04 - 1.24: 1121 1.24 - 1.44: 2771 1.44 - 1.64: 5220 1.64 - 1.84: 82 Bond restraints: 18416 Sorted by residual: bond pdb=" CB MET H 85 " pdb=" CG MET H 85 " ideal model delta sigma weight residual 1.520 1.594 -0.074 3.00e-02 1.11e+03 6.15e+00 bond pdb=" N GLY G 1 " pdb=" CA GLY G 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.43e+00 bond pdb=" N GLY G 1 " pdb=" H GLY G 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 18411 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.84: 198 105.84 - 113.04: 21851 113.04 - 120.24: 6001 120.24 - 127.45: 5246 127.45 - 134.65: 118 Bond angle restraints: 33414 Sorted by residual: angle pdb=" CG MET H 85 " pdb=" SD MET H 85 " pdb=" CE MET H 85 " ideal model delta sigma weight residual 100.90 110.19 -9.29 2.20e+00 2.07e-01 1.78e+01 angle pdb=" CB MET H 85 " pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 112.70 125.31 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N MET H 85 " pdb=" CA MET H 85 " pdb=" CB MET H 85 " ideal model delta sigma weight residual 111.56 117.41 -5.85 1.58e+00 4.01e-01 1.37e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CD PRO A 204 " ideal model delta sigma weight residual 120.60 113.40 7.20 2.20e+00 2.07e-01 1.07e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 127.00 134.65 -7.65 2.40e+00 1.74e-01 1.02e+01 ... (remaining 33409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7447 17.10 - 34.19: 762 34.19 - 51.29: 266 51.29 - 68.39: 98 68.39 - 85.48: 7 Dihedral angle restraints: 8580 sinusoidal: 4602 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LEU B 24 " pdb=" C LEU B 24 " pdb=" N ILE B 25 " pdb=" CA ILE B 25 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" N MET A 203 " pdb=" CA MET A 203 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 197 " pdb=" C LEU A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1040 0.035 - 0.071: 288 0.071 - 0.106: 99 0.106 - 0.142: 32 0.142 - 0.177: 3 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ARG G 55 " pdb=" N ARG G 55 " pdb=" C ARG G 55 " pdb=" CB ARG G 55 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1459 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 255 " 0.025 2.00e-02 2.50e+03 1.79e-02 1.29e+01 pdb=" CG TRP A 255 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 255 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 255 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 255 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 255 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 255 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 55 " 0.295 9.50e-02 1.11e+02 9.88e-02 1.10e+01 pdb=" NE ARG G 55 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 55 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 55 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 55 " 0.010 2.00e-02 2.50e+03 pdb="HH11 ARG G 55 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG G 55 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 55 " -0.012 2.00e-02 2.50e+03 pdb="HH22 ARG G 55 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 335 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 336 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.041 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1308 2.20 - 2.80: 38234 2.80 - 3.40: 52285 3.40 - 4.00: 65943 4.00 - 4.60: 102050 Nonbonded interactions: 259820 Sorted by model distance: nonbonded pdb=" OE1 GLU A 287 " pdb=" H GLU A 287 " model vdw 1.605 1.850 nonbonded pdb=" O MET E 40 " pdb=" H MET E 44 " model vdw 1.641 1.850 nonbonded pdb=" O LEU B 19 " pdb=" HG SER B 22 " model vdw 1.654 1.850 nonbonded pdb="HE22 GLN E 307 " pdb=" O PHE E 319 " model vdw 1.680 1.850 nonbonded pdb="HH12 ARG E 314 " pdb=" OE1 GLN E 316 " model vdw 1.681 1.850 ... (remaining 259815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.050 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: 0.250 Extract box with map and model: 4.470 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 59.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 0.074 9188 Z= 0.199 Angle : 0.614 12.613 12508 Z= 0.312 Chirality : 0.040 0.177 1462 Planarity : 0.007 0.128 1546 Dihedral : 15.732 84.149 3236 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.10 % Allowed : 19.52 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.87 (0.25), residues: 1136 helix: 1.11 (0.21), residues: 630 sheet: 0.53 (0.57), residues: 92 loop : -0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 255 HIS 0.004 0.001 HIS A 8 PHE 0.023 0.001 PHE A 319 TYR 0.018 0.001 TYR E 176 ARG 0.009 0.001 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7369 (tp40) cc_final: 0.7154 (tp40) REVERT: A 329 GLU cc_start: 0.7078 (tp30) cc_final: 0.6797 (tp30) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.4964 time to fit residues: 198.4308 Evaluate side-chains 293 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9188 Z= 0.253 Angle : 0.590 6.562 12508 Z= 0.307 Chirality : 0.041 0.185 1462 Planarity : 0.006 0.138 1546 Dihedral : 4.619 33.175 1235 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.09 % Allowed : 17.95 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.74 (0.25), residues: 1136 helix: 1.07 (0.20), residues: 656 sheet: 0.26 (0.53), residues: 92 loop : -0.32 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 255 HIS 0.004 0.001 HIS A 325 PHE 0.016 0.001 PHE F 96 TYR 0.011 0.001 TYR A 149 ARG 0.011 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 322 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.6951 (tp30) cc_final: 0.6679 (tp30) REVERT: E 119 LYS cc_start: 0.7900 (tptt) cc_final: 0.7668 (tptt) REVERT: H 77 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6509 (mm110) outliers start: 20 outliers final: 15 residues processed: 327 average time/residue: 0.4894 time to fit residues: 219.0268 Evaluate side-chains 332 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 317 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9188 Z= 0.480 Angle : 0.683 6.605 12508 Z= 0.374 Chirality : 0.045 0.212 1462 Planarity : 0.006 0.114 1546 Dihedral : 5.081 28.951 1232 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.24 % Allowed : 17.85 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.07 (0.24), residues: 1136 helix: 0.35 (0.19), residues: 668 sheet: 0.08 (0.52), residues: 92 loop : -0.57 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 39 HIS 0.010 0.001 HIS A 325 PHE 0.024 0.002 PHE A 207 TYR 0.021 0.002 TYR F 71 ARG 0.015 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 337 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 162 VAL cc_start: 0.8734 (t) cc_final: 0.8467 (m) REVERT: A 283 LEU cc_start: 0.8384 (mt) cc_final: 0.8110 (mt) REVERT: E 1 MET cc_start: 0.6278 (mmm) cc_final: 0.5995 (mmm) REVERT: E 138 SER cc_start: 0.8133 (p) cc_final: 0.7920 (p) REVERT: E 321 MET cc_start: 0.6579 (mtp) cc_final: 0.6257 (mtp) REVERT: B 50 MET cc_start: 0.7164 (tpp) cc_final: 0.6950 (tpp) REVERT: F 73 GLU cc_start: 0.7648 (mp0) cc_final: 0.7402 (mp0) REVERT: F 89 GLU cc_start: 0.7375 (tp30) cc_final: 0.7133 (tp30) outliers start: 31 outliers final: 23 residues processed: 343 average time/residue: 0.5049 time to fit residues: 234.8492 Evaluate side-chains 348 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 324 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9188 Z= 0.220 Angle : 0.566 6.824 12508 Z= 0.292 Chirality : 0.040 0.186 1462 Planarity : 0.005 0.109 1546 Dihedral : 4.665 33.187 1232 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.92 % Allowed : 20.67 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1136 helix: 0.76 (0.20), residues: 668 sheet: -0.05 (0.51), residues: 92 loop : -0.52 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 39 HIS 0.003 0.001 HIS A 325 PHE 0.015 0.001 PHE H 96 TYR 0.012 0.001 TYR A 149 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 323 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8141 (tt) cc_final: 0.7781 (mt) REVERT: A 283 LEU cc_start: 0.8397 (mt) cc_final: 0.8120 (mt) REVERT: A 329 GLU cc_start: 0.7046 (tp30) cc_final: 0.6797 (tp30) REVERT: E 1 MET cc_start: 0.6205 (mmm) cc_final: 0.5915 (mmm) REVERT: E 116 ASP cc_start: 0.6822 (m-30) cc_final: 0.6521 (m-30) REVERT: E 321 MET cc_start: 0.6456 (mtp) cc_final: 0.6237 (mtp) REVERT: F 89 GLU cc_start: 0.7449 (tp30) cc_final: 0.7225 (tp30) REVERT: H 102 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6941 (tm-30) outliers start: 28 outliers final: 25 residues processed: 332 average time/residue: 0.5114 time to fit residues: 231.7099 Evaluate side-chains 347 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 321 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9188 Z= 0.224 Angle : 0.551 6.779 12508 Z= 0.285 Chirality : 0.040 0.179 1462 Planarity : 0.005 0.084 1546 Dihedral : 4.565 35.653 1232 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.24 % Allowed : 20.98 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.50 (0.25), residues: 1136 helix: 0.91 (0.20), residues: 667 sheet: -0.08 (0.51), residues: 92 loop : -0.46 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 39 HIS 0.005 0.001 HIS A 325 PHE 0.021 0.001 PHE H 96 TYR 0.014 0.001 TYR A 232 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 319 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 VAL cc_start: 0.8707 (t) cc_final: 0.8412 (p) REVERT: A 283 LEU cc_start: 0.8388 (mt) cc_final: 0.8135 (mt) REVERT: E 1 MET cc_start: 0.6105 (mmm) cc_final: 0.5761 (mmm) REVERT: E 116 ASP cc_start: 0.6813 (m-30) cc_final: 0.6494 (m-30) REVERT: E 321 MET cc_start: 0.6429 (mtp) cc_final: 0.6015 (mtp) REVERT: E 341 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7203 (mmt-90) REVERT: B 42 ARG cc_start: 0.6677 (tmm-80) cc_final: 0.6385 (tmm-80) REVERT: G 24 LEU cc_start: 0.8427 (mt) cc_final: 0.8143 (mp) REVERT: G 55 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6002 (mtp85) REVERT: F 89 GLU cc_start: 0.7565 (tp30) cc_final: 0.7342 (tp30) REVERT: H 85 MET cc_start: 0.2984 (ptt) cc_final: 0.2193 (pmm) REVERT: H 102 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6965 (tm-30) outliers start: 31 outliers final: 20 residues processed: 330 average time/residue: 0.5075 time to fit residues: 226.0989 Evaluate side-chains 336 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9188 Z= 0.263 Angle : 0.563 6.835 12508 Z= 0.294 Chirality : 0.041 0.181 1462 Planarity : 0.005 0.084 1546 Dihedral : 4.630 37.454 1232 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.65 % Allowed : 20.25 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.48 (0.25), residues: 1136 helix: 0.90 (0.20), residues: 667 sheet: -0.11 (0.52), residues: 92 loop : -0.46 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 39 HIS 0.006 0.001 HIS A 325 PHE 0.023 0.001 PHE H 96 TYR 0.020 0.002 TYR A 134 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 323 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8247 (mt) cc_final: 0.8045 (mp) REVERT: A 36 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 98 VAL cc_start: 0.8715 (t) cc_final: 0.8431 (p) REVERT: A 283 LEU cc_start: 0.8381 (mt) cc_final: 0.8131 (mt) REVERT: E 1 MET cc_start: 0.6088 (mmm) cc_final: 0.5759 (mmm) REVERT: E 116 ASP cc_start: 0.6778 (m-30) cc_final: 0.6443 (m-30) REVERT: E 321 MET cc_start: 0.6345 (mtp) cc_final: 0.5970 (mtp) REVERT: E 341 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7300 (mmt-90) REVERT: B 42 ARG cc_start: 0.6648 (tmm-80) cc_final: 0.6337 (tmm-80) REVERT: G 24 LEU cc_start: 0.8447 (mt) cc_final: 0.8161 (mp) REVERT: F 89 GLU cc_start: 0.7628 (tp30) cc_final: 0.7393 (tp30) outliers start: 35 outliers final: 26 residues processed: 334 average time/residue: 0.4806 time to fit residues: 216.6658 Evaluate side-chains 350 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 322 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9188 Z= 0.300 Angle : 0.575 6.787 12508 Z= 0.304 Chirality : 0.041 0.196 1462 Planarity : 0.005 0.075 1546 Dihedral : 4.722 38.236 1232 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.13 % Allowed : 21.19 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.39 (0.25), residues: 1136 helix: 0.85 (0.20), residues: 665 sheet: -0.06 (0.52), residues: 92 loop : -0.59 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 39 HIS 0.006 0.001 HIS A 325 PHE 0.024 0.002 PHE H 96 TYR 0.020 0.002 TYR A 232 ARG 0.003 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 323 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8248 (mt) cc_final: 0.8045 (mp) REVERT: A 36 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 98 VAL cc_start: 0.8713 (t) cc_final: 0.8432 (p) REVERT: A 283 LEU cc_start: 0.8405 (mt) cc_final: 0.8137 (mt) REVERT: E 1 MET cc_start: 0.6023 (mmm) cc_final: 0.5707 (mmm) REVERT: E 53 PHE cc_start: 0.7679 (m-80) cc_final: 0.7465 (m-80) REVERT: E 116 ASP cc_start: 0.6775 (m-30) cc_final: 0.6437 (m-30) REVERT: E 137 MET cc_start: 0.7453 (mtp) cc_final: 0.7037 (ttp) REVERT: E 299 VAL cc_start: 0.8209 (p) cc_final: 0.7987 (t) REVERT: E 341 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7387 (mmt-90) REVERT: B 42 ARG cc_start: 0.6368 (tmm-80) cc_final: 0.5981 (tmm-80) REVERT: G 24 LEU cc_start: 0.8491 (mt) cc_final: 0.8156 (mp) REVERT: F 89 GLU cc_start: 0.7679 (tp30) cc_final: 0.7436 (tp30) outliers start: 30 outliers final: 23 residues processed: 335 average time/residue: 0.4957 time to fit residues: 224.5510 Evaluate side-chains 347 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 322 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9188 Z= 0.236 Angle : 0.554 6.785 12508 Z= 0.288 Chirality : 0.040 0.176 1462 Planarity : 0.005 0.075 1546 Dihedral : 4.597 38.391 1232 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.82 % Allowed : 21.61 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1136 helix: 1.00 (0.20), residues: 665 sheet: -0.06 (0.52), residues: 92 loop : -0.58 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 39 HIS 0.004 0.001 HIS A 325 PHE 0.024 0.001 PHE H 96 TYR 0.021 0.001 TYR A 232 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 322 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8251 (mt) cc_final: 0.8037 (mp) REVERT: A 36 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 98 VAL cc_start: 0.8695 (t) cc_final: 0.8408 (p) REVERT: A 283 LEU cc_start: 0.8403 (mt) cc_final: 0.8152 (mt) REVERT: E 1 MET cc_start: 0.6008 (mmm) cc_final: 0.5702 (mmm) REVERT: E 116 ASP cc_start: 0.6756 (m-30) cc_final: 0.6411 (m-30) REVERT: E 267 ASP cc_start: 0.6963 (m-30) cc_final: 0.6701 (m-30) REVERT: E 299 VAL cc_start: 0.8203 (p) cc_final: 0.7986 (t) REVERT: E 341 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7301 (mmt-90) REVERT: G 24 LEU cc_start: 0.8469 (mt) cc_final: 0.8146 (mp) REVERT: G 44 LEU cc_start: 0.8080 (tp) cc_final: 0.7870 (tt) REVERT: F 73 GLU cc_start: 0.7422 (mp0) cc_final: 0.7142 (mp0) REVERT: F 89 GLU cc_start: 0.7720 (tp30) cc_final: 0.7459 (tp30) REVERT: H 102 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6999 (tm-30) outliers start: 27 outliers final: 21 residues processed: 330 average time/residue: 0.5046 time to fit residues: 225.0237 Evaluate side-chains 343 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9188 Z= 0.205 Angle : 0.542 6.771 12508 Z= 0.279 Chirality : 0.040 0.173 1462 Planarity : 0.005 0.065 1546 Dihedral : 4.503 38.758 1232 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.82 % Allowed : 22.34 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.65 (0.25), residues: 1136 helix: 1.09 (0.20), residues: 665 sheet: -0.02 (0.52), residues: 92 loop : -0.51 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 39 HIS 0.004 0.001 HIS F 116 PHE 0.022 0.001 PHE H 96 TYR 0.020 0.001 TYR A 232 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 316 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8223 (mt) cc_final: 0.8016 (mp) REVERT: A 36 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (mt) REVERT: A 88 LEU cc_start: 0.8355 (mm) cc_final: 0.8130 (mt) REVERT: A 98 VAL cc_start: 0.8688 (t) cc_final: 0.8405 (p) REVERT: A 197 LEU cc_start: 0.7612 (mt) cc_final: 0.7399 (mt) REVERT: A 283 LEU cc_start: 0.8392 (mt) cc_final: 0.8135 (mt) REVERT: A 329 GLU cc_start: 0.6890 (tp30) cc_final: 0.6667 (tp30) REVERT: E 1 MET cc_start: 0.5979 (mmm) cc_final: 0.5691 (mmm) REVERT: E 116 ASP cc_start: 0.6706 (m-30) cc_final: 0.6321 (m-30) REVERT: E 267 ASP cc_start: 0.6948 (m-30) cc_final: 0.6687 (m-30) REVERT: E 299 VAL cc_start: 0.8196 (p) cc_final: 0.7966 (t) REVERT: E 341 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7255 (mmt-90) REVERT: G 24 LEU cc_start: 0.8471 (mt) cc_final: 0.8158 (mp) REVERT: F 73 GLU cc_start: 0.7344 (mp0) cc_final: 0.7029 (mp0) REVERT: F 89 GLU cc_start: 0.7744 (tp30) cc_final: 0.7466 (tp30) outliers start: 27 outliers final: 25 residues processed: 324 average time/residue: 0.5244 time to fit residues: 231.3930 Evaluate side-chains 342 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 315 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9188 Z= 0.248 Angle : 0.555 6.702 12508 Z= 0.290 Chirality : 0.040 0.180 1462 Planarity : 0.005 0.075 1546 Dihedral : 4.567 38.886 1232 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.82 % Allowed : 22.65 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.58 (0.25), residues: 1136 helix: 1.04 (0.20), residues: 665 sheet: -0.02 (0.52), residues: 92 loop : -0.57 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 39 HIS 0.005 0.001 HIS A 325 PHE 0.023 0.001 PHE H 96 TYR 0.021 0.001 TYR A 232 ARG 0.003 0.000 ARG G 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 321 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8234 (mt) cc_final: 0.8022 (mp) REVERT: A 36 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7872 (mt) REVERT: A 88 LEU cc_start: 0.8395 (mm) cc_final: 0.8151 (mt) REVERT: A 98 VAL cc_start: 0.8703 (t) cc_final: 0.8418 (p) REVERT: A 283 LEU cc_start: 0.8407 (mt) cc_final: 0.8154 (mt) REVERT: A 329 GLU cc_start: 0.6898 (tp30) cc_final: 0.6682 (tp30) REVERT: E 1 MET cc_start: 0.5963 (mmm) cc_final: 0.5690 (mmm) REVERT: E 116 ASP cc_start: 0.6711 (m-30) cc_final: 0.6334 (m-30) REVERT: E 267 ASP cc_start: 0.6967 (m-30) cc_final: 0.6705 (m-30) REVERT: E 299 VAL cc_start: 0.8197 (p) cc_final: 0.7976 (t) REVERT: E 341 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7320 (mmt-90) REVERT: G 24 LEU cc_start: 0.8516 (mt) cc_final: 0.8177 (mp) REVERT: F 73 GLU cc_start: 0.7398 (mp0) cc_final: 0.7100 (mp0) REVERT: F 89 GLU cc_start: 0.7799 (tp30) cc_final: 0.7538 (tp30) REVERT: F 131 LYS cc_start: 0.5948 (ptpp) cc_final: 0.5675 (ptpp) outliers start: 27 outliers final: 23 residues processed: 329 average time/residue: 0.5123 time to fit residues: 228.4282 Evaluate side-chains 346 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 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 = 0.3992 r_free = 0.3992 target = 0.154575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120590 restraints weight = 40946.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125900 restraints weight = 13942.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128856 restraints weight = 7132.064| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9188 Z= 0.211 Angle : 0.546 6.720 12508 Z= 0.281 Chirality : 0.040 0.173 1462 Planarity : 0.005 0.068 1546 Dihedral : 4.505 39.401 1232 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.61 % Allowed : 22.96 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.66 (0.25), residues: 1136 helix: 1.13 (0.20), residues: 665 sheet: -0.00 (0.52), residues: 92 loop : -0.57 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 39 HIS 0.007 0.001 HIS F 123 PHE 0.021 0.001 PHE H 96 TYR 0.021 0.001 TYR A 232 ARG 0.006 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.97 seconds wall clock time: 91 minutes 13.78 seconds (5473.78 seconds total)