Starting phenix.real_space_refine on Tue Feb 13 22:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpt_34943/02_2024/8hpt_34943_updated.pdb" } resolution = 3.39 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= 0.024 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 48 5.16 5 C 5051 2.51 5 N 1343 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7897 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1872 Classifications: {'peptide': 255} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 62 Classifications: {'peptide': 6} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'ZAL:plan-1': 1, 'ALC:plan-1': 1, 'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1458 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 48} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2436 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 8, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 395 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1674 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 4.75, per 1000 atoms: 0.60 Number of scatterers: 7897 At special positions: 0 Unit cell: (89.0706, 126.025, 128.868, 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 48 16.00 O 1455 8.00 N 1343 7.00 C 5051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR D 406 " Input volumes are d-peptide like pdb=" CB ZAL D 404 " Number of C-beta restraints generated: 2032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 15 sheets defined 34.4% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 37 through 64 Proline residue: A 53 - end of helix removed outlier: 4.507A pdb=" N PHE A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 97 removed outlier: 4.309A pdb=" N TRP A 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 3.550A pdb=" N THR A 94 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 96 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 139 Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 150 through 173 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 202 through 232 removed outlier: 5.591A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 4.208A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 240 through 265 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 277 through 304 removed outlier: 4.681A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.970A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 209 through 216 removed outlier: 4.616A pdb=" N HIS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 216 " --> pdb=" O TRP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.747A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.523A pdb=" N GLN G 11 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN G 24 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.805A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.956A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.569A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.589A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 229 through 234 removed outlier: 7.074A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.416A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.726A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.118A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 78 through 83 removed outlier: 3.802A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'H' and resid 93 through 98 removed outlier: 3.592A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.667A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL H 149 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLU H 246 " --> pdb=" O VAL H 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.523A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 225 through 231 removed outlier: 6.214A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 960 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: 2.37 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1277 1.32 - 1.44: 2223 1.44 - 1.56: 4498 1.56 - 1.69: 1 1.69 - 1.81: 65 Bond restraints: 8064 Sorted by residual: bond pdb=" C PRO A 298 " pdb=" O PRO A 298 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.00e-02 1.00e+04 1.72e+01 bond pdb=" N LEU A 276 " pdb=" CA LEU A 276 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" C PRO A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.45e+00 bond pdb=" C PRO A 170 " pdb=" O PRO A 170 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.26e-02 6.30e+03 6.57e+00 bond pdb=" N ASP H 223 " pdb=" CA ASP H 223 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.81e+00 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 186 106.41 - 113.31: 4416 113.31 - 120.21: 2714 120.21 - 127.11: 3610 127.11 - 134.01: 85 Bond angle restraints: 11011 Sorted by residual: angle pdb=" N PRO A 170 " pdb=" CA PRO A 170 " pdb=" C PRO A 170 " ideal model delta sigma weight residual 113.53 108.21 5.32 1.39e+00 5.18e-01 1.47e+01 angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" O ILE A 169 " pdb=" C ILE A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 121.10 117.10 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" CB MET H 83 " pdb=" CG MET H 83 " pdb=" SD MET H 83 " ideal model delta sigma weight residual 112.70 122.36 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CA ASP H 223 " pdb=" CB ASP H 223 " pdb=" CG ASP H 223 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 ... (remaining 11006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.57: 4427 26.57 - 53.13: 229 53.13 - 79.70: 15 79.70 - 106.27: 2 106.27 - 132.83: 2 Dihedral angle restraints: 4675 sinusoidal: 1525 harmonic: 3150 Sorted by residual: dihedral pdb=" CD DAR D 406 " pdb=" NE DAR D 406 " pdb=" CZ DAR D 406 " pdb=" NH1 DAR D 406 " ideal model delta sinusoidal sigma weight residual 0.00 -132.83 132.83 1 1.00e+01 1.00e-02 1.61e+02 dihedral pdb=" CA GLY A 51 " pdb=" C GLY A 51 " pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CG ALC D 405 " pdb=" CD1 ALC D 405 " pdb=" CE1 ALC D 405 " pdb=" CZ ALC D 405 " ideal model delta sinusoidal sigma weight residual -55.84 61.55 -117.39 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 4672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1028 0.047 - 0.095: 219 0.095 - 0.142: 56 0.142 - 0.190: 2 0.190 - 0.237: 2 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA DAR D 406 " pdb=" N DAR D 406 " pdb=" C DAR D 406 " pdb=" CB DAR D 406 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A 266 " pdb=" CA ILE A 266 " pdb=" CG1 ILE A 266 " pdb=" CG2 ILE A 266 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1304 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD DAR D 406 " 0.801 9.50e-02 1.11e+02 3.59e-01 7.84e+01 pdb=" NE DAR D 406 " -0.047 2.00e-02 2.50e+03 pdb=" CZ DAR D 406 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 DAR D 406 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 DAR D 406 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO H 14 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 74 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO H 75 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 75 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 75 " 0.047 5.00e-02 4.00e+02 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 843 2.75 - 3.29: 7662 3.29 - 3.82: 12807 3.82 - 4.36: 13887 4.36 - 4.90: 25620 Nonbonded interactions: 60819 Sorted by model distance: nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.212 2.440 nonbonded pdb=" O SER B 310 " pdb=" OG SER B 310 " model vdw 2.226 2.440 nonbonded pdb=" NH1 ARG H 180 " pdb=" O GLU H 222 " model vdw 2.306 2.520 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR C 128 " pdb=" O ASN C 132 " model vdw 2.351 2.440 ... (remaining 60814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.300 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: 9.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 0.045 8064 Z= 0.173 Angle : 0.598 9.662 11011 Z= 0.315 Chirality : 0.042 0.237 1307 Planarity : 0.011 0.359 1398 Dihedral : 14.890 132.831 2637 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.40 % Allowed : 8.30 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.29 (0.27), residues: 1067 helix: 1.87 (0.28), residues: 364 sheet: -0.21 (0.32), residues: 291 loop : -1.00 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 268 HIS 0.003 0.001 HIS B 189 PHE 0.025 0.001 PHE H 68 TYR 0.017 0.001 TYR B 297 ARG 0.006 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.890 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.2140 time to fit residues: 27.8059 Evaluate side-chains 93 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8064 Z= 0.338 Angle : 0.634 7.578 11011 Z= 0.328 Chirality : 0.045 0.179 1307 Planarity : 0.005 0.059 1398 Dihedral : 7.602 179.719 1170 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.01 % Allowed : 13.65 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.27), residues: 1067 helix: 1.54 (0.29), residues: 362 sheet: -0.22 (0.31), residues: 302 loop : -1.05 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 74 HIS 0.007 0.002 HIS C 142 PHE 0.042 0.002 PHE H 68 TYR 0.018 0.002 TYR H 190 ARG 0.004 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.753 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.1897 time to fit residues: 29.9999 Evaluate side-chains 110 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.1980 chunk 29 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8064 Z= 0.182 Angle : 0.529 7.022 11011 Z= 0.272 Chirality : 0.041 0.168 1307 Planarity : 0.004 0.049 1398 Dihedral : 7.294 178.614 1170 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.28 % Allowed : 17.67 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.27), residues: 1067 helix: 1.48 (0.29), residues: 362 sheet: -0.14 (0.31), residues: 294 loop : -1.03 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 74 HIS 0.002 0.001 HIS B 189 PHE 0.032 0.001 PHE H 68 TYR 0.011 0.001 TYR H 101 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.828 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 115 average time/residue: 0.1844 time to fit residues: 29.4110 Evaluate side-chains 115 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.0070 chunk 102 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 194 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8064 Z= 0.155 Angle : 0.509 7.918 11011 Z= 0.259 Chirality : 0.040 0.152 1307 Planarity : 0.004 0.045 1398 Dihedral : 7.143 179.855 1170 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 19.41 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.20 (0.27), residues: 1067 helix: 1.57 (0.29), residues: 362 sheet: -0.11 (0.31), residues: 305 loop : -0.94 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS C 142 PHE 0.029 0.001 PHE H 68 TYR 0.014 0.001 TYR B 297 ARG 0.004 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.789 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.1940 time to fit residues: 31.4806 Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.0010 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8064 Z= 0.161 Angle : 0.504 7.026 11011 Z= 0.257 Chirality : 0.041 0.170 1307 Planarity : 0.004 0.043 1398 Dihedral : 6.957 179.436 1169 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.81 % Allowed : 20.88 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.26 (0.27), residues: 1067 helix: 1.60 (0.29), residues: 358 sheet: -0.08 (0.31), residues: 305 loop : -0.87 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS C 142 PHE 0.031 0.001 PHE H 68 TYR 0.010 0.001 TYR H 190 ARG 0.004 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.896 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.1861 time to fit residues: 30.7663 Evaluate side-chains 120 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8064 Z= 0.201 Angle : 0.528 7.692 11011 Z= 0.269 Chirality : 0.041 0.171 1307 Planarity : 0.004 0.042 1398 Dihedral : 6.997 179.207 1169 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.75 % Allowed : 20.21 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.24 (0.27), residues: 1067 helix: 1.57 (0.29), residues: 358 sheet: -0.07 (0.31), residues: 303 loop : -0.87 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 74 HIS 0.004 0.001 HIS C 142 PHE 0.036 0.001 PHE H 68 TYR 0.016 0.001 TYR B 297 ARG 0.008 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.932 Fit side-chains outliers start: 28 outliers final: 23 residues processed: 129 average time/residue: 0.1870 time to fit residues: 33.4795 Evaluate side-chains 126 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN C 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8064 Z= 0.210 Angle : 0.529 7.172 11011 Z= 0.272 Chirality : 0.042 0.185 1307 Planarity : 0.004 0.041 1398 Dihedral : 7.018 179.211 1169 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.75 % Allowed : 20.62 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.20 (0.27), residues: 1067 helix: 1.50 (0.29), residues: 360 sheet: -0.12 (0.31), residues: 304 loop : -0.84 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 74 HIS 0.003 0.001 HIS C 142 PHE 0.037 0.001 PHE H 68 TYR 0.011 0.001 TYR H 190 ARG 0.007 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.834 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 121 average time/residue: 0.1892 time to fit residues: 31.5251 Evaluate side-chains 125 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.0010 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 92 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 overall best weight: 0.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8064 Z= 0.121 Angle : 0.490 7.179 11011 Z= 0.248 Chirality : 0.040 0.202 1307 Planarity : 0.004 0.038 1398 Dihedral : 6.831 179.805 1169 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 22.76 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.34 (0.27), residues: 1067 helix: 1.61 (0.29), residues: 357 sheet: 0.01 (0.31), residues: 303 loop : -0.79 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 74 HIS 0.004 0.001 HIS C 183 PHE 0.028 0.001 PHE H 68 TYR 0.018 0.001 TYR B 297 ARG 0.007 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.903 Fit side-chains REVERT: B 23 LEU cc_start: 0.8375 (mp) cc_final: 0.8170 (mt) outliers start: 16 outliers final: 15 residues processed: 117 average time/residue: 0.1945 time to fit residues: 31.0442 Evaluate side-chains 114 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.0000 chunk 100 optimal weight: 0.0770 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8064 Z= 0.155 Angle : 0.506 8.744 11011 Z= 0.256 Chirality : 0.040 0.132 1307 Planarity : 0.004 0.041 1398 Dihedral : 6.841 179.626 1169 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.28 % Allowed : 22.62 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.27), residues: 1067 helix: 1.60 (0.29), residues: 359 sheet: 0.03 (0.31), residues: 304 loop : -0.78 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.004 0.001 HIS C 183 PHE 0.029 0.001 PHE H 68 TYR 0.016 0.001 TYR B 297 ARG 0.008 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.973 Fit side-chains REVERT: A 265 MET cc_start: 0.7773 (tpp) cc_final: 0.7421 (tpp) outliers start: 17 outliers final: 17 residues processed: 113 average time/residue: 0.2006 time to fit residues: 31.1402 Evaluate side-chains 117 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8064 Z= 0.174 Angle : 0.522 9.583 11011 Z= 0.263 Chirality : 0.041 0.133 1307 Planarity : 0.004 0.039 1398 Dihedral : 6.891 179.612 1169 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.28 % Allowed : 23.16 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.35 (0.27), residues: 1067 helix: 1.58 (0.29), residues: 359 sheet: -0.01 (0.31), residues: 307 loop : -0.73 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.005 0.001 HIS C 183 PHE 0.029 0.001 PHE H 68 TYR 0.015 0.001 TYR B 297 ARG 0.009 0.000 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.933 Fit side-chains REVERT: A 265 MET cc_start: 0.7819 (tpp) cc_final: 0.7428 (tpp) REVERT: G 21 MET cc_start: 0.7912 (tmm) cc_final: 0.7608 (mmm) outliers start: 17 outliers final: 16 residues processed: 112 average time/residue: 0.1898 time to fit residues: 29.4805 Evaluate side-chains 114 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN C 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135108 restraints weight = 9842.075| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.41 r_work: 0.3376 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8064 Z= 0.246 Angle : 0.558 9.226 11011 Z= 0.284 Chirality : 0.042 0.138 1307 Planarity : 0.004 0.039 1398 Dihedral : 7.030 179.160 1169 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.68 % Allowed : 22.62 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.27), residues: 1067 helix: 1.52 (0.28), residues: 359 sheet: -0.09 (0.31), residues: 313 loop : -0.77 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.007 0.001 HIS C 183 PHE 0.037 0.002 PHE H 68 TYR 0.014 0.001 TYR B 297 ARG 0.009 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.48 seconds wall clock time: 37 minutes 13.89 seconds (2233.89 seconds total)