Starting phenix.real_space_refine on Sat Apr 6 17:39:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trp_26100/04_2024/7trp_26100_updated.pdb" } resolution = 2.4 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= 0.002 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 64 5.16 5 Cl 1 4.86 5 C 5535 2.51 5 N 1461 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8681 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2079 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2591 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1768 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'IUE': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.02, per 1000 atoms: 0.58 Number of scatterers: 8681 At special positions: 0 Unit cell: (93.79, 119.52, 123.67, 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) Cl 1 17.00 S 64 16.00 O 1620 8.00 N 1461 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 33.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'R' and resid 34 through 59 Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.384A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 Processing helix chain 'R' and resid 103 through 135 Processing helix chain 'R' and resid 146 through 174 Proline residue: R 166 - end of helix removed outlier: 5.184A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 222 Processing helix chain 'R' and resid 393 through 425 Proline residue: R 415 - end of helix removed outlier: 3.537A pdb=" N THR R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 447 removed outlier: 3.798A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Processing helix chain 'R' and resid 449 through 453 Processing helix chain 'R' and resid 458 through 462 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 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 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.792A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.289A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.923A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.994A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.648A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.016A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.691A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.563A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.841A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.496A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.502A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1155 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: 2.79 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1398 1.31 - 1.44: 2469 1.44 - 1.57: 4903 1.57 - 1.69: 1 1.69 - 1.82: 94 Bond restraints: 8865 Sorted by residual: bond pdb=" C10 IXO R 702 " pdb=" N11 IXO R 702 " ideal model delta sigma weight residual 1.270 1.475 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C10 IXO R 702 " pdb=" C14 IXO R 702 " ideal model delta sigma weight residual 1.492 1.331 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C13 IXO R 702 " pdb=" O12 IXO R 702 " ideal model delta sigma weight residual 1.439 1.544 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C05 IXO R 702 " pdb=" C06 IXO R 702 " ideal model delta sigma weight residual 1.450 1.528 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C07 IXO R 702 " pdb=" C08 IXO R 702 " ideal model delta sigma weight residual 1.454 1.530 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 59.93 - 83.94: 3 83.94 - 107.95: 357 107.95 - 131.96: 11654 131.96 - 155.97: 25 155.97 - 179.97: 2 Bond angle restraints: 12041 Sorted by residual: angle pdb=" N GLY H 209 " pdb=" CA GLY H 209 " pdb=" C GLY H 209 " ideal model delta sigma weight residual 113.18 121.40 -8.22 2.37e+00 1.78e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N ALA R 165 " pdb=" CA ALA R 165 " pdb=" C ALA R 165 " ideal model delta sigma weight residual 112.75 117.28 -4.53 1.36e+00 5.41e-01 1.11e+01 angle pdb=" CA TRP R 440 " pdb=" CB TRP R 440 " pdb=" CG TRP R 440 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.05e+01 angle pdb=" N CYS R 429 " pdb=" CA CYS R 429 " pdb=" C CYS R 429 " ideal model delta sigma weight residual 111.07 114.38 -3.31 1.07e+00 8.73e-01 9.54e+00 ... (remaining 12036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4906 16.99 - 33.98: 270 33.98 - 50.97: 45 50.97 - 67.96: 9 67.96 - 84.95: 4 Dihedral angle restraints: 5234 sinusoidal: 1974 harmonic: 3260 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1099 0.064 - 0.127: 225 0.127 - 0.191: 53 0.191 - 0.255: 5 0.255 - 0.318: 3 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB THR R 90 " pdb=" CA THR R 90 " pdb=" OG1 THR R 90 " pdb=" CG2 THR R 90 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1382 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUE R 701 " 0.035 2.00e-02 2.50e+03 3.45e-02 4.17e+01 pdb=" C IUE R 701 " -0.023 2.00e-02 2.50e+03 pdb=" O IUE R 701 " -0.039 2.00e-02 2.50e+03 pdb=" C1 IUE R 701 " 0.013 2.00e-02 2.50e+03 pdb=" C2 IUE R 701 " 0.029 2.00e-02 2.50e+03 pdb=" C3 IUE R 701 " 0.014 2.00e-02 2.50e+03 pdb=" C4 IUE R 701 " -0.012 2.00e-02 2.50e+03 pdb=" C5 IUE R 701 " 0.036 2.00e-02 2.50e+03 pdb=" C6 IUE R 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 IUE R 701 " -0.003 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " -0.086 2.00e-02 2.50e+03 pdb=" N2 IUE R 701 " 0.046 2.00e-02 2.50e+03 pdb=" S IUE R 701 " 0.016 2.00e-02 2.50e+03 pdb="CL IUE R 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IUE R 701 " -0.057 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C4 IUE R 701 " -0.045 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " 0.021 2.00e-02 2.50e+03 pdb=" N1 IUE R 701 " 0.076 2.00e-02 2.50e+03 pdb=" O1 IUE R 701 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 113 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C TYR R 113 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR R 113 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL R 114 " -0.022 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2328 2.81 - 3.33: 7749 3.33 - 3.85: 14676 3.85 - 4.38: 17729 4.38 - 4.90: 30356 Nonbonded interactions: 72838 Sorted by model distance: nonbonded pdb=" OH TYR R 113 " pdb=" OH TYR R 416 " model vdw 2.287 2.440 nonbonded pdb=" O THR R 433 " pdb=" OG SER R 436 " model vdw 2.311 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.324 2.440 nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.329 2.440 ... (remaining 72833 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.390 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.006 0.205 8865 Z= 0.386 Angle : 0.818 9.994 12041 Z= 0.464 Chirality : 0.056 0.318 1385 Planarity : 0.007 0.085 1511 Dihedral : 11.233 84.947 3118 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.43 (0.23), residues: 1106 helix: -0.02 (0.24), residues: 382 sheet: 0.22 (0.29), residues: 300 loop : -0.74 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 440 HIS 0.004 0.001 HIS H 35 PHE 0.035 0.003 PHE R 189 TYR 0.029 0.002 TYR R 215 ARG 0.006 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: R 210 ILE cc_start: 0.8052 (mm) cc_final: 0.7814 (mp) REVERT: R 223 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7722 (ttm110) REVERT: B 270 ILE cc_start: 0.9015 (pt) cc_final: 0.8768 (tp) REVERT: H 186 GLN cc_start: 0.8733 (tt0) cc_final: 0.8461 (tt0) REVERT: H 220 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7958 (mm-30) REVERT: A 302 TYR cc_start: 0.8938 (t80) cc_final: 0.8697 (t80) REVERT: A 306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8296 (mp10) REVERT: A 308 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8352 (mt-10) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 1.7815 time to fit residues: 303.8506 Evaluate side-chains 123 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 ASN R 117 ASN R 172 GLN B 268 ASN B 340 ASN H 39 GLN A 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8865 Z= 0.234 Angle : 0.518 6.118 12041 Z= 0.281 Chirality : 0.041 0.139 1385 Planarity : 0.004 0.054 1511 Dihedral : 4.856 43.387 1225 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.83 % Allowed : 9.02 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1106 helix: 1.77 (0.26), residues: 382 sheet: 0.64 (0.29), residues: 298 loop : -0.23 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.008 0.001 HIS A 188 PHE 0.016 0.001 PHE R 189 TYR 0.013 0.001 TYR R 89 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8533 (p) REVERT: G 15 LEU cc_start: 0.8699 (tt) cc_final: 0.8431 (tm) REVERT: H 160 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7703 (ttp80) REVERT: H 186 GLN cc_start: 0.8677 (tt0) cc_final: 0.8326 (tt0) REVERT: A 306 GLN cc_start: 0.8892 (mm110) cc_final: 0.8339 (mp10) REVERT: A 308 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8330 (mt-10) outliers start: 17 outliers final: 1 residues processed: 140 average time/residue: 1.6766 time to fit residues: 246.2747 Evaluate side-chains 115 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.252 Angle : 0.528 6.076 12041 Z= 0.283 Chirality : 0.041 0.139 1385 Planarity : 0.004 0.046 1511 Dihedral : 4.587 21.931 1225 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.15 % Allowed : 11.39 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1106 helix: 2.07 (0.27), residues: 384 sheet: 0.61 (0.29), residues: 303 loop : -0.07 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 84 TYR 0.014 0.001 TYR R 89 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (p) REVERT: R 136 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8152 (mttm) REVERT: R 184 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7525 (mm-40) REVERT: G 15 LEU cc_start: 0.8698 (tt) cc_final: 0.8436 (tm) REVERT: H 186 GLN cc_start: 0.8688 (tt0) cc_final: 0.8348 (tt0) REVERT: A 306 GLN cc_start: 0.8849 (mm110) cc_final: 0.8343 (mp10) outliers start: 20 outliers final: 8 residues processed: 126 average time/residue: 1.5923 time to fit residues: 210.9359 Evaluate side-chains 121 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8865 Z= 0.253 Angle : 0.528 6.074 12041 Z= 0.283 Chirality : 0.041 0.139 1385 Planarity : 0.004 0.046 1511 Dihedral : 4.587 21.931 1225 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.18 % Allowed : 13.10 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1106 helix: 2.07 (0.27), residues: 384 sheet: 0.61 (0.29), residues: 303 loop : -0.07 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 84 TYR 0.014 0.001 TYR R 89 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8528 (p) REVERT: R 136 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8152 (mttm) REVERT: R 184 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7525 (mm-40) REVERT: G 15 LEU cc_start: 0.8698 (tt) cc_final: 0.8436 (tm) REVERT: H 186 GLN cc_start: 0.8688 (tt0) cc_final: 0.8348 (tt0) REVERT: A 306 GLN cc_start: 0.8849 (mm110) cc_final: 0.8343 (mp10) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 1.5751 time to fit residues: 195.6476 Evaluate side-chains 121 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8865 Z= 0.253 Angle : 0.528 6.074 12041 Z= 0.283 Chirality : 0.041 0.139 1385 Planarity : 0.004 0.046 1511 Dihedral : 4.587 21.931 1225 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.18 % Allowed : 13.10 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1106 helix: 2.07 (0.27), residues: 384 sheet: 0.61 (0.29), residues: 303 loop : -0.07 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 84 TYR 0.014 0.001 TYR R 89 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8528 (p) REVERT: R 136 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8152 (mttm) REVERT: R 184 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7525 (mm-40) REVERT: G 15 LEU cc_start: 0.8698 (tt) cc_final: 0.8436 (tm) REVERT: H 186 GLN cc_start: 0.8688 (tt0) cc_final: 0.8348 (tt0) REVERT: A 306 GLN cc_start: 0.8849 (mm110) cc_final: 0.8343 (mp10) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 1.6005 time to fit residues: 198.6500 Evaluate side-chains 121 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8865 Z= 0.165 Angle : 0.510 8.174 12041 Z= 0.271 Chirality : 0.040 0.142 1385 Planarity : 0.004 0.045 1511 Dihedral : 4.426 21.163 1225 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.72 % Allowed : 12.78 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1106 helix: 2.20 (0.27), residues: 387 sheet: 0.66 (0.30), residues: 294 loop : -0.03 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.017 0.001 PHE R 84 TYR 0.021 0.001 TYR A 296 ARG 0.008 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8049 (mttm) REVERT: G 15 LEU cc_start: 0.8678 (tt) cc_final: 0.8420 (tm) REVERT: H 186 GLN cc_start: 0.8675 (tt0) cc_final: 0.8338 (tt0) REVERT: A 306 GLN cc_start: 0.8846 (mm110) cc_final: 0.8323 (mp10) outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 1.5486 time to fit residues: 199.1644 Evaluate side-chains 118 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 427 GLN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 296 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8865 Z= 0.180 Angle : 0.514 8.558 12041 Z= 0.271 Chirality : 0.040 0.141 1385 Planarity : 0.003 0.043 1511 Dihedral : 4.331 20.389 1225 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.29 % Allowed : 13.96 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1106 helix: 2.25 (0.27), residues: 386 sheet: 0.68 (0.30), residues: 288 loop : -0.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE R 84 TYR 0.020 0.001 TYR A 296 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8008 (mttm) REVERT: R 184 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7483 (mm-40) REVERT: G 15 LEU cc_start: 0.8675 (tt) cc_final: 0.8416 (tm) REVERT: H 186 GLN cc_start: 0.8679 (tt0) cc_final: 0.8347 (tt0) REVERT: A 306 GLN cc_start: 0.8835 (mm110) cc_final: 0.8319 (mp10) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 1.5598 time to fit residues: 208.6574 Evaluate side-chains 124 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 427 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8865 Z= 0.180 Angle : 0.514 8.558 12041 Z= 0.271 Chirality : 0.040 0.141 1385 Planarity : 0.003 0.043 1511 Dihedral : 4.330 20.389 1225 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.07 % Allowed : 14.39 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1106 helix: 2.25 (0.27), residues: 386 sheet: 0.68 (0.30), residues: 288 loop : -0.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE R 84 TYR 0.020 0.001 TYR A 296 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8008 (mttm) REVERT: R 184 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7483 (mm-40) REVERT: G 15 LEU cc_start: 0.8675 (tt) cc_final: 0.8416 (tm) REVERT: H 186 GLN cc_start: 0.8679 (tt0) cc_final: 0.8347 (tt0) REVERT: A 306 GLN cc_start: 0.8836 (mm110) cc_final: 0.8319 (mp10) outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 1.6385 time to fit residues: 209.9785 Evaluate side-chains 124 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 427 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8865 Z= 0.293 Angle : 0.570 9.007 12041 Z= 0.300 Chirality : 0.042 0.142 1385 Planarity : 0.004 0.044 1511 Dihedral : 4.494 20.265 1225 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.40 % Allowed : 14.07 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 388 sheet: 0.66 (0.30), residues: 292 loop : 0.04 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.002 PHE R 189 TYR 0.023 0.002 TYR A 296 ARG 0.010 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 148 MET cc_start: 0.7225 (mmp) cc_final: 0.6874 (mmm) REVERT: R 184 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: G 15 LEU cc_start: 0.8710 (tt) cc_final: 0.8479 (tm) REVERT: H 186 GLN cc_start: 0.8689 (tt0) cc_final: 0.8375 (tt0) REVERT: A 306 GLN cc_start: 0.8892 (mm110) cc_final: 0.8403 (mp10) outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 1.5576 time to fit residues: 213.3541 Evaluate side-chains 125 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 427 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN A 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8865 Z= 0.293 Angle : 0.570 9.006 12041 Z= 0.300 Chirality : 0.042 0.142 1385 Planarity : 0.004 0.044 1511 Dihedral : 4.495 20.265 1225 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.97 % Allowed : 15.25 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 388 sheet: 0.66 (0.30), residues: 292 loop : 0.04 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.002 PHE R 189 TYR 0.023 0.002 TYR A 296 ARG 0.010 0.001 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 148 MET cc_start: 0.7217 (mmp) cc_final: 0.6874 (mmm) REVERT: R 184 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: G 15 LEU cc_start: 0.8710 (tt) cc_final: 0.8479 (tm) REVERT: H 186 GLN cc_start: 0.8689 (tt0) cc_final: 0.8375 (tt0) REVERT: A 306 GLN cc_start: 0.8896 (mm110) cc_final: 0.8403 (mp10) outliers start: 9 outliers final: 7 residues processed: 124 average time/residue: 1.6085 time to fit residues: 209.7501 Evaluate side-chains 125 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 427 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 36 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN A 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.064454 restraints weight = 14594.395| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.66 r_work: 0.2674 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8865 Z= 0.293 Angle : 0.570 9.006 12041 Z= 0.300 Chirality : 0.042 0.142 1385 Planarity : 0.004 0.044 1511 Dihedral : 4.494 20.265 1225 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.97 % Allowed : 15.25 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 388 sheet: 0.66 (0.30), residues: 292 loop : 0.04 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.002 PHE R 189 TYR 0.023 0.002 TYR A 296 ARG 0.010 0.001 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.89 seconds wall clock time: 78 minutes 11.04 seconds (4691.04 seconds total)