Starting phenix.real_space_refine (version: dev) on Mon Apr 4 19:16:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_2022/7ljc_23390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljc_23390/04_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-4553/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: 6.44, per 1000 atoms: 0.75 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: 3.61 Conformation dependent library (CDL) restraints added in 1.6 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: 0.77 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: 2.61 Time building geometry restraints manager: 3.88 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=" C04 SK0 R 501 " pdb="CL01 SK0 R 501 " ideal model delta sigma weight residual 1.787 1.720 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C02 SK0 R 501 " pdb=" C09 SK0 R 501 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.80e+00 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=" C05 SK0 R 501 " pdb=" O01 SK0 R 501 " ideal model delta sigma weight residual 1.400 1.358 0.042 2.00e-02 2.50e+03 4.48e+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=" C01 SK0 R 501 " pdb=" C02 SK0 R 501 " pdb=" C09 SK0 R 501 " ideal model delta sigma weight residual 110.99 123.31 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C02 SK0 R 501 " pdb=" C01 SK0 R 501 " pdb=" C07 SK0 R 501 " ideal model delta sigma weight residual 110.98 121.69 -10.71 3.00e+00 1.11e-01 1.27e+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 ... (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: 150 0.183 - 0.274: 11 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: 0.230 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: 2.030 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 27.690 Find NCS groups from input model: 0.250 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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= 0.340 Angle : 1.013 12.321 11829 Z= 0.546 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 : 5.07 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 : 1.005 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 0.9546 time to fit residues: 302.1501 Evaluate side-chains 255 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1295 time to fit residues: 1.5339 ------------------------------------------------------------------------------- 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 41 ASN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 8730 Z= 0.218 Angle : 0.578 14.673 11829 Z= 0.297 Chirality : 0.041 0.189 1331 Planarity : 0.005 0.060 1458 Dihedral : 5.892 86.915 1278 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.24 (0.25), residues: 1024 helix: 1.90 (0.23), residues: 411 sheet: -0.35 (0.33), residues: 230 loop : -1.47 (0.27), residues: 383 *********************** 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 275 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 260 average time/residue: 1.0974 time to fit residues: 305.3635 Evaluate side-chains 240 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.8053 time to fit residues: 5.6814 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 130 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8730 Z= 0.189 Angle : 0.568 18.322 11829 Z= 0.281 Chirality : 0.040 0.144 1331 Planarity : 0.005 0.063 1458 Dihedral : 5.474 84.468 1278 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.12 % 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 (0.25), residues: 1024 helix: 2.02 (0.25), residues: 414 sheet: -0.20 (0.34), residues: 202 loop : -1.20 (0.27), residues: 408 *********************** 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 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 238 average time/residue: 1.0536 time to fit residues: 268.8332 Evaluate side-chains 236 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 223 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 5 average time/residue: 0.7331 time to fit residues: 5.4682 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8730 Z= 0.236 Angle : 0.560 19.589 11829 Z= 0.279 Chirality : 0.040 0.131 1331 Planarity : 0.005 0.080 1458 Dihedral : 5.465 84.358 1278 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.60 (0.25), residues: 1024 helix: 1.94 (0.25), residues: 414 sheet: -0.13 (0.34), residues: 207 loop : -0.93 (0.29), residues: 403 *********************** 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 254 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 242 average time/residue: 1.0935 time to fit residues: 283.1090 Evaluate side-chains 240 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 7 average time/residue: 0.2570 time to fit residues: 3.6455 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 160 GLN A 19 GLN A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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: 0.8285 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 8730 Z= 0.308 Angle : 0.591 20.377 11829 Z= 0.294 Chirality : 0.041 0.131 1331 Planarity : 0.005 0.067 1458 Dihedral : 5.662 85.153 1278 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.35 % 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: 0.53 (0.26), residues: 1024 helix: 1.79 (0.25), residues: 414 sheet: -0.29 (0.33), residues: 215 loop : -0.78 (0.30), residues: 395 *********************** 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 266 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 253 average time/residue: 1.0818 time to fit residues: 292.5058 Evaluate side-chains 238 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 7 average time/residue: 0.5555 time to fit residues: 5.7102 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 88 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 8730 Z= 0.257 Angle : 0.591 20.821 11829 Z= 0.287 Chirality : 0.040 0.131 1331 Planarity : 0.005 0.065 1458 Dihedral : 5.557 84.219 1278 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.46 % 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: 0.46 (0.26), residues: 1024 helix: 1.73 (0.25), residues: 416 sheet: -0.47 (0.33), residues: 217 loop : -0.74 (0.31), residues: 391 *********************** 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 254 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 0.965 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 242 average time/residue: 1.1269 time to fit residues: 290.9800 Evaluate side-chains 242 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 7 average time/residue: 0.3544 time to fit residues: 4.3252 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 230 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: 0.8257 moved from start: 0.3798 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= 0.194 Angle : 0.569 20.707 11829 Z= 0.277 Chirality : 0.040 0.133 1331 Planarity : 0.005 0.057 1458 Dihedral : 5.355 82.205 1278 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 2.91 % 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: 0.51 (0.26), residues: 1024 helix: 1.82 (0.25), residues: 414 sheet: -0.56 (0.32), residues: 236 loop : -0.67 (0.32), residues: 374 *********************** 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 260 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 244 average time/residue: 1.1374 time to fit residues: 296.7496 Evaluate side-chains 245 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 227 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 9 average time/residue: 0.3811 time to fit residues: 5.4532 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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: 0.8260 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8730 Z= 0.214 Angle : 0.577 20.484 11829 Z= 0.282 Chirality : 0.040 0.132 1331 Planarity : 0.005 0.070 1458 Dihedral : 5.319 81.591 1278 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.46 % 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: 0.49 (0.26), residues: 1024 helix: 1.79 (0.25), residues: 414 sheet: -0.62 (0.32), residues: 236 loop : -0.61 (0.32), residues: 374 *********************** 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 262 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 250 average time/residue: 1.0868 time to fit residues: 290.8156 Evaluate side-chains 261 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 8 average time/residue: 0.1295 time to fit residues: 2.9183 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.0040 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 110 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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: 0.8265 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8730 Z= 0.234 Angle : 0.593 20.938 11829 Z= 0.288 Chirality : 0.040 0.149 1331 Planarity : 0.005 0.079 1458 Dihedral : 5.307 78.648 1278 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.35 % 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: 0.54 (0.26), residues: 1024 helix: 1.85 (0.25), residues: 411 sheet: -0.70 (0.32), residues: 236 loop : -0.49 (0.33), residues: 377 *********************** 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 250 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 237 average time/residue: 1.1458 time to fit residues: 289.7233 Evaluate side-chains 249 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 8 average time/residue: 0.6602 time to fit residues: 7.3072 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 110 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN N 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8730 Z= 0.225 Angle : 0.595 20.923 11829 Z= 0.288 Chirality : 0.040 0.145 1331 Planarity : 0.005 0.088 1458 Dihedral : 5.273 77.025 1278 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.35 % 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: 0.55 (0.26), residues: 1024 helix: 1.85 (0.25), residues: 407 sheet: -0.68 (0.32), residues: 239 loop : -0.46 (0.33), residues: 378 ********************** 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 243 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 232 average time/residue: 1.1683 time to fit residues: 288.7948 Evaluate side-chains 234 residues out of total 895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.8620 time to fit residues: 6.8654 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129214 restraints weight = 11226.695| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.88 r_work: 0.3558 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3529 rms_B_bonded: 1.73 restraints_weight: 0.1250 r_work: 0.3514 rms_B_bonded: 1.83 restraints_weight: 0.0625 r_work: 0.3498 rms_B_bonded: 1.97 restraints_weight: 0.0312 r_work: 0.3480 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.3460 rms_B_bonded: 2.36 restraints_weight: 0.0078 r_work: 0.3439 rms_B_bonded: 2.62 restraints_weight: 0.0039 r_work: 0.3416 rms_B_bonded: 2.92 restraints_weight: 0.0020 r_work: 0.3390 rms_B_bonded: 3.27 restraints_weight: 0.0010 r_work: 0.3362 rms_B_bonded: 3.68 restraints_weight: 0.0005 r_work: 0.3330 rms_B_bonded: 4.15 restraints_weight: 0.0002 r_work: 0.3295 rms_B_bonded: 4.69 restraints_weight: 0.0001 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8730 Z= 0.190 Angle : 0.587 22.138 11829 Z= 0.283 Chirality : 0.039 0.158 1331 Planarity : 0.005 0.097 1458 Dihedral : 5.120 72.386 1278 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.12 % 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: 1.74 (0.25), residues: 418 sheet: -0.64 (0.32), residues: 238 loop : -0.53 (0.33), residues: 368 =============================================================================== Job complete usr+sys time: 4295.47 seconds wall clock time: 76 minutes 31.09 seconds (4591.09 seconds total)