Starting phenix.real_space_refine (version: dev) on Thu May 12 22:15:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/05_2022/7ljc_23390_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.037 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 Convert atoms to be neutral 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-4597/modules/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2226 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1989 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 326 Unusual residues: {'PLM': 6, 'G4C': 1, 'SK0': 1, 'CLR': 6} Classifications: {'undetermined': 14} Link IDs: {None: 13} Time building chain proxies: 5.36, per 1000 atoms: 0.63 Number of scatterers: 8544 At special positions: 0 Unit cell: (91.96, 108.68, 123.31, 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 3 17.00 S 55 16.00 O 1539 8.00 N 1442 7.00 C 5505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.34 Conformation dependent library (CDL) restraints added in 1.3 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 22 through 50 Processing helix chain 'R' and resid 52 through 55 No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 59 through 76 removed outlier: 4.168A pdb=" N LEU R 76 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.902A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS R 106 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER R 107 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU R 112 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.294A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'R' and resid 204 through 239 Processing helix chain 'R' and resid 265 through 297 removed outlier: 3.696A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 310 through 331 removed outlier: 3.975A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 345 Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 96 through 102 removed outlier: 3.621A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.829A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 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 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 211 through 215 removed outlier: 7.157A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.278A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.094A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.855A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.073A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.012A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1077 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: 2.35 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2148 1.33 - 1.46: 1881 1.46 - 1.58: 4623 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8730 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.498 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.02e+00 bond pdb=" C ASN R 327 " pdb=" N PRO R 328 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.64e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.21e+00 bond pdb=" C LEU R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.18e+00 ... (remaining 8725 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.69: 158 105.69 - 112.79: 4709 112.79 - 119.89: 2876 119.89 - 126.98: 3980 126.98 - 134.08: 106 Bond angle restraints: 11829 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N GLY B 244 " pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 113.18 105.26 7.92 2.37e+00 1.78e-01 1.12e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.06 114.24 -5.18 1.70e+00 3.46e-01 9.28e+00 ... (remaining 11824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5020 17.55 - 35.09: 114 35.09 - 52.64: 20 52.64 - 70.18: 2 70.18 - 87.73: 2 Dihedral angle restraints: 5158 sinusoidal: 2122 harmonic: 3036 Sorted by residual: dihedral pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1158 0.091 - 0.183: 149 0.183 - 0.274: 12 0.274 - 0.366: 6 0.366 - 0.457: 6 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 1328 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " 0.225 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" C05 G4C R 502 " -0.051 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " 0.180 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " -0.036 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " -0.227 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 101 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ALA R 101 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA R 101 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 102 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 110 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER R 110 " -0.068 2.00e-02 2.50e+03 pdb=" O SER R 110 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 111 " 0.023 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2113 2.81 - 3.33: 7674 3.33 - 3.85: 14366 3.85 - 4.38: 16591 4.38 - 4.90: 28853 Nonbonded interactions: 69597 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.288 2.440 nonbonded pdb=" OG SER R 198 " pdb=" O02 SK0 R 501 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR R 59 " pdb=" OH TYR R 131 " model vdw 2.371 2.440 nonbonded pdb=" NH2 ARG R 133 " pdb=" O LYS A 78 " model vdw 2.371 2.520 ... (remaining 69592 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 3 4.86 5 C 5505 2.51 5 N 1442 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.000 Extract box with map and model: 2.010 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 25.280 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.005 0.143 8730 Z= 0.333 Angle : 1.005 9.518 11829 Z= 0.544 Chirality : 0.068 0.457 1331 Planarity : 0.009 0.156 1458 Dihedral : 8.580 87.728 3174 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1024 helix: 0.47 (0.21), residues: 389 sheet: -0.65 (0.32), residues: 239 loop : -1.87 (0.26), residues: 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 0.9224 time to fit residues: 292.2065 Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1317 time to fit residues: 1.5282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 164 HIS R 222 GLN A 19 GLN A 75 GLN B 62 HIS B 88 ASN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 8730 Z= 0.230 Angle : 0.561 14.886 11829 Z= 0.294 Chirality : 0.041 0.157 1331 Planarity : 0.005 0.060 1458 Dihedral : 5.881 85.980 1278 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1024 helix: 1.99 (0.23), residues: 405 sheet: -0.35 (0.33), residues: 230 loop : -1.48 (0.27), residues: 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 252 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 261 average time/residue: 1.1005 time to fit residues: 306.8123 Evaluate side-chains 243 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.8123 time to fit residues: 5.7743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 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 41 ASN A 19 GLN A 130 ASN A 131 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 8730 Z= 0.217 Angle : 0.557 18.827 11829 Z= 0.283 Chirality : 0.041 0.143 1331 Planarity : 0.005 0.063 1458 Dihedral : 5.541 85.154 1278 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1024 helix: 1.93 (0.24), residues: 414 sheet: -0.27 (0.34), residues: 203 loop : -1.14 (0.27), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 238 average time/residue: 1.0497 time to fit residues: 267.2924 Evaluate side-chains 238 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 6 average time/residue: 0.6017 time to fit residues: 5.3066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 8730 Z= 0.270 Angle : 0.552 19.874 11829 Z= 0.281 Chirality : 0.040 0.127 1331 Planarity : 0.005 0.076 1458 Dihedral : 5.592 85.172 1278 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1024 helix: 1.87 (0.25), residues: 414 sheet: -0.34 (0.34), residues: 204 loop : -0.87 (0.29), residues: 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 249 average time/residue: 1.0808 time to fit residues: 287.7513 Evaluate side-chains 242 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 231 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.5947 time to fit residues: 4.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8730 Z= 0.197 Angle : 0.531 19.837 11829 Z= 0.267 Chirality : 0.040 0.133 1331 Planarity : 0.005 0.062 1458 Dihedral : 5.393 83.219 1278 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1024 helix: 1.91 (0.25), residues: 414 sheet: -0.34 (0.34), residues: 212 loop : -0.72 (0.30), residues: 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 253 average time/residue: 1.0697 time to fit residues: 289.6856 Evaluate side-chains 244 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.1554 time to fit residues: 2.4238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 236 GLN B 17 GLN B 88 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8730 Z= 0.202 Angle : 0.540 17.709 11829 Z= 0.271 Chirality : 0.040 0.131 1331 Planarity : 0.005 0.066 1458 Dihedral : 5.358 82.440 1278 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1024 helix: 1.84 (0.25), residues: 416 sheet: -0.34 (0.33), residues: 227 loop : -0.67 (0.31), residues: 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 251 average time/residue: 1.1122 time to fit residues: 298.0416 Evaluate side-chains 244 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 7 average time/residue: 0.2955 time to fit residues: 3.7960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8730 Z= 0.179 Angle : 0.544 19.352 11829 Z= 0.271 Chirality : 0.039 0.133 1331 Planarity : 0.005 0.073 1458 Dihedral : 5.195 80.577 1278 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1024 helix: 1.98 (0.25), residues: 409 sheet: -0.50 (0.33), residues: 236 loop : -0.67 (0.31), residues: 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 237 average time/residue: 1.1041 time to fit residues: 279.8224 Evaluate side-chains 237 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 225 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.1378 time to fit residues: 2.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 8730 Z= 0.263 Angle : 0.573 20.005 11829 Z= 0.287 Chirality : 0.041 0.140 1331 Planarity : 0.005 0.085 1458 Dihedral : 5.316 78.569 1278 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1024 helix: 1.72 (0.25), residues: 414 sheet: -0.54 (0.33), residues: 216 loop : -0.68 (0.31), residues: 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 0.995 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 246 average time/residue: 1.1069 time to fit residues: 290.7975 Evaluate side-chains 247 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 7 average time/residue: 0.2651 time to fit residues: 3.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8730 Z= 0.276 Angle : 0.613 22.979 11829 Z= 0.298 Chirality : 0.041 0.153 1331 Planarity : 0.005 0.088 1458 Dihedral : 5.346 76.672 1278 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1024 helix: 1.69 (0.25), residues: 414 sheet: -0.57 (0.32), residues: 230 loop : -0.55 (0.32), residues: 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 1.041 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 241 average time/residue: 1.1150 time to fit residues: 286.5448 Evaluate side-chains 237 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 227 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.1559 time to fit residues: 1.7548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8730 Z= 0.272 Angle : 0.604 21.959 11829 Z= 0.297 Chirality : 0.041 0.152 1331 Planarity : 0.005 0.085 1458 Dihedral : 5.350 75.643 1278 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1024 helix: 1.64 (0.25), residues: 413 sheet: -0.60 (0.32), residues: 230 loop : -0.53 (0.32), residues: 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 0.968 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 238 average time/residue: 1.1089 time to fit residues: 281.7475 Evaluate side-chains 239 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 0.5335 time to fit residues: 4.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 53 HIS A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130343 restraints weight = 11211.396| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.87 r_work: 0.3566 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.3537 rms_B_bonded: 1.72 restraints_weight: 0.1250 r_work: 0.3522 rms_B_bonded: 1.82 restraints_weight: 0.0625 r_work: 0.3506 rms_B_bonded: 1.96 restraints_weight: 0.0312 r_work: 0.3488 rms_B_bonded: 2.14 restraints_weight: 0.0156 r_work: 0.3468 rms_B_bonded: 2.36 restraints_weight: 0.0078 r_work: 0.3447 rms_B_bonded: 2.61 restraints_weight: 0.0039 r_work: 0.3424 rms_B_bonded: 2.91 restraints_weight: 0.0020 r_work: 0.3398 rms_B_bonded: 3.26 restraints_weight: 0.0010 r_work: 0.3370 rms_B_bonded: 3.67 restraints_weight: 0.0005 r_work: 0.3338 rms_B_bonded: 4.14 restraints_weight: 0.0002 r_work: 0.3303 rms_B_bonded: 4.67 restraints_weight: 0.0001 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8730 Z= 0.171 Angle : 0.583 22.236 11829 Z= 0.285 Chirality : 0.039 0.152 1331 Planarity : 0.005 0.089 1458 Dihedral : 5.128 71.950 1278 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1024 helix: 1.69 (0.25), residues: 419 sheet: -0.59 (0.33), residues: 229 loop : -0.53 (0.32), residues: 376 =============================================================================== Job complete usr+sys time: 4228.35 seconds wall clock time: 75 minutes 19.32 seconds (4519.32 seconds total)