Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 07:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk5_25173/04_2023/7sk5_25173_trim_updated.pdb" } resolution = 4.0 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= -0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4713 2.51 5 N 1163 2.21 5 O 1317 1.98 5 H 6928 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14160 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4915 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "F" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3248 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1058 Classifications: {'peptide': 63} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "E" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3206 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1537 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 4 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.85, per 1000 atoms: 0.48 Number of scatterers: 14160 At special positions: 0 Unit cell: (59.4, 90.72, 160.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1317 8.00 N 1163 7.00 C 4713 6.00 H 6928 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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: 10.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 13 sheets defined 28.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 3.546A pdb=" N GLY A 58 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 62 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.723A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.759A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 181 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.787A pdb=" N ILE A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS A 206 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 218 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.152A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 253 through 279 removed outlier: 4.131A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 287 through 315 removed outlier: 4.244A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.578A pdb=" N GLU E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 184 through 189' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.605A pdb=" N LYS A 184 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 197 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 6 through 10 Processing sheet with id= C, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.770A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER F 53 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.713A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.862A pdb=" N CYS F 213 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS F 226 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 27 through 31 Processing sheet with id= G, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.690A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 20 through 25 Processing sheet with id= I, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.652A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.195A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.442A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 17 through 22 removed outlier: 3.747A pdb=" N THR K 69 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.764A pdb=" N MET K 34 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 693 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: 4.72 Time building geometry restraints manager: 11.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6918 1.03 - 1.23: 43 1.23 - 1.43: 3101 1.43 - 1.62: 4245 1.62 - 1.82: 52 Bond restraints: 14359 Sorted by residual: bond pdb=" C6 CLR A 401 " pdb=" C7 CLR A 401 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C6 CLR A 406 " pdb=" C7 CLR A 406 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C6 CLR F 301 " pdb=" C7 CLR F 301 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C6 CLR A 405 " pdb=" C7 CLR A 405 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C6 CLR A 403 " pdb=" C7 CLR A 403 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 14354 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.64: 150 104.64 - 112.00: 16150 112.00 - 119.36: 3298 119.36 - 126.71: 6061 126.71 - 134.07: 132 Bond angle restraints: 25791 Sorted by residual: angle pdb=" C22 CLR A 405 " pdb=" C23 CLR A 405 " pdb=" C24 CLR A 405 " ideal model delta sigma weight residual 111.95 104.13 7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C22 CLR A 401 " pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " ideal model delta sigma weight residual 111.95 104.19 7.76 3.00e+00 1.11e-01 6.70e+00 angle pdb=" C22 CLR A 406 " pdb=" C23 CLR A 406 " pdb=" C24 CLR A 406 " ideal model delta sigma weight residual 111.95 104.35 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" C22 CLR A 404 " pdb=" C23 CLR A 404 " pdb=" C24 CLR A 404 " ideal model delta sigma weight residual 111.95 104.50 7.45 3.00e+00 1.11e-01 6.17e+00 angle pdb=" C22 CLR F 301 " pdb=" C23 CLR F 301 " pdb=" C24 CLR F 301 " ideal model delta sigma weight residual 111.95 104.68 7.27 3.00e+00 1.11e-01 5.87e+00 ... (remaining 25786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5342 17.15 - 34.29: 424 34.29 - 51.44: 73 51.44 - 68.59: 11 68.59 - 85.74: 11 Dihedral angle restraints: 5861 sinusoidal: 2646 harmonic: 3215 Sorted by residual: dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual 93.00 62.15 30.85 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA ARG E 62 " pdb=" CB ARG E 62 " pdb=" CG ARG E 62 " pdb=" CD ARG E 62 " ideal model delta sinusoidal sigma weight residual 180.00 129.14 50.86 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PHE K 103 " pdb=" C PHE K 103 " pdb=" N TYR K 104 " pdb=" CA TYR K 104 " ideal model delta harmonic sigma weight residual 180.00 165.16 14.84 0 5.00e+00 4.00e-02 8.81e+00 ... (remaining 5858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1049 0.075 - 0.150: 98 0.150 - 0.225: 0 0.225 - 0.300: 10 0.300 - 0.375: 18 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C17 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C16 CLR A 405 " pdb=" C20 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C17 CLR F 301 " pdb=" C13 CLR F 301 " pdb=" C16 CLR F 301 " pdb=" C20 CLR F 301 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1172 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 141 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 142 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 142 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 142 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 120 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO E 121 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 9 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO B 10 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.017 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 664 2.19 - 2.79: 27381 2.79 - 3.39: 36639 3.39 - 4.00: 47145 4.00 - 4.60: 71663 Nonbonded interactions: 183492 Sorted by model distance: nonbonded pdb=" OE1 GLU A 202 " pdb=" H GLU A 202 " model vdw 1.583 1.850 nonbonded pdb=" HD1 HIS F 217 " pdb=" OG SER F 220 " model vdw 1.621 1.850 nonbonded pdb=" OH TYR F 63 " pdb=" H ILE F 73 " model vdw 1.634 1.850 nonbonded pdb=" O ALA F 27 " pdb="HD22 ASN F 80 " model vdw 1.636 1.850 nonbonded pdb=" OD1 ASN F 31 " pdb=" H SER F 33 " model vdw 1.647 1.850 ... (remaining 183487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.220 Extract box with map and model: 8.510 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 44.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.004 0.050 7431 Z= 0.281 Angle : 0.628 7.824 10157 Z= 0.265 Chirality : 0.063 0.375 1175 Planarity : 0.003 0.036 1219 Dihedral : 13.926 85.737 2600 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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 (0.29), residues: 875 helix: 2.24 (0.33), residues: 235 sheet: 0.24 (0.34), residues: 252 loop : -0.79 (0.33), residues: 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3889 time to fit residues: 87.0414 Evaluate side-chains 141 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 80 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7431 Z= 0.166 Angle : 0.521 5.159 10157 Z= 0.285 Chirality : 0.041 0.142 1175 Planarity : 0.005 0.055 1219 Dihedral : 4.744 43.677 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.10 (0.29), residues: 875 helix: 1.32 (0.34), residues: 237 sheet: 0.08 (0.32), residues: 267 loop : -0.69 (0.34), residues: 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 155 average time/residue: 0.3618 time to fit residues: 77.5833 Evaluate side-chains 152 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1770 time to fit residues: 3.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7431 Z= 0.237 Angle : 0.530 5.354 10157 Z= 0.284 Chirality : 0.040 0.146 1175 Planarity : 0.004 0.046 1219 Dihedral : 4.842 43.255 1034 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.18 (0.29), residues: 875 helix: 1.01 (0.34), residues: 239 sheet: -0.02 (0.33), residues: 260 loop : -0.86 (0.33), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 150 average time/residue: 0.3591 time to fit residues: 74.9027 Evaluate side-chains 146 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1560 time to fit residues: 3.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7431 Z= 0.248 Angle : 0.535 6.313 10157 Z= 0.285 Chirality : 0.040 0.163 1175 Planarity : 0.004 0.041 1219 Dihedral : 4.916 41.253 1034 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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 (0.29), residues: 875 helix: 0.98 (0.35), residues: 233 sheet: -0.10 (0.33), residues: 262 loop : -0.84 (0.33), residues: 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 147 average time/residue: 0.3603 time to fit residues: 73.5657 Evaluate side-chains 146 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.082 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1578 time to fit residues: 2.7355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7431 Z= 0.274 Angle : 0.551 7.168 10157 Z= 0.292 Chirality : 0.040 0.158 1175 Planarity : 0.004 0.033 1219 Dihedral : 5.007 39.657 1034 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.32 (0.29), residues: 875 helix: 0.93 (0.35), residues: 233 sheet: -0.18 (0.32), residues: 262 loop : -0.89 (0.33), residues: 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 147 average time/residue: 0.3547 time to fit residues: 72.3302 Evaluate side-chains 146 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.155 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1616 time to fit residues: 2.8569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7431 Z= 0.175 Angle : 0.511 8.152 10157 Z= 0.268 Chirality : 0.040 0.149 1175 Planarity : 0.004 0.032 1219 Dihedral : 4.842 41.272 1034 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.21 (0.29), residues: 875 helix: 1.13 (0.36), residues: 232 sheet: -0.20 (0.32), residues: 266 loop : -0.81 (0.34), residues: 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.3720 time to fit residues: 77.2080 Evaluate side-chains 152 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.050 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1657 time to fit residues: 3.2848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7431 Z= 0.217 Angle : 0.530 8.716 10157 Z= 0.277 Chirality : 0.040 0.149 1175 Planarity : 0.004 0.031 1219 Dihedral : 4.865 43.601 1034 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.23 (0.29), residues: 875 helix: 1.13 (0.36), residues: 232 sheet: -0.16 (0.32), residues: 273 loop : -0.89 (0.34), residues: 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.3604 time to fit residues: 73.0262 Evaluate side-chains 143 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.149 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1848 time to fit residues: 2.0708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7431 Z= 0.185 Angle : 0.518 9.544 10157 Z= 0.270 Chirality : 0.040 0.151 1175 Planarity : 0.004 0.031 1219 Dihedral : 4.804 45.918 1034 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.15 (0.29), residues: 875 helix: 1.20 (0.36), residues: 232 sheet: -0.11 (0.32), residues: 273 loop : -0.85 (0.34), residues: 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 147 average time/residue: 0.3684 time to fit residues: 75.6316 Evaluate side-chains 146 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.184 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1882 time to fit residues: 2.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 7431 Z= 0.288 Angle : 0.566 9.518 10157 Z= 0.298 Chirality : 0.040 0.151 1175 Planarity : 0.004 0.032 1219 Dihedral : 5.043 48.895 1034 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: -0.28 (0.29), residues: 875 helix: 1.02 (0.35), residues: 232 sheet: -0.18 (0.32), residues: 271 loop : -0.88 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 138 average time/residue: 0.3683 time to fit residues: 70.5625 Evaluate side-chains 138 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.254 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1557 time to fit residues: 2.0315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7431 Z= 0.209 Angle : 0.536 9.748 10157 Z= 0.279 Chirality : 0.040 0.164 1175 Planarity : 0.004 0.035 1219 Dihedral : 4.983 52.026 1034 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 875 helix: 1.09 (0.35), residues: 232 sheet: -0.15 (0.32), residues: 271 loop : -0.82 (0.34), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 143 average time/residue: 0.3777 time to fit residues: 74.1907 Evaluate side-chains 142 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.072 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1441 time to fit residues: 2.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102026 restraints weight = 37285.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106543 restraints weight = 15341.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109329 restraints weight = 8929.202| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7431 Z= 0.153 Angle : 0.501 9.323 10157 Z= 0.259 Chirality : 0.040 0.165 1175 Planarity : 0.003 0.030 1219 Dihedral : 4.793 54.258 1034 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.30), residues: 875 helix: 1.31 (0.35), residues: 237 sheet: -0.04 (0.32), residues: 271 loop : -0.89 (0.34), residues: 367 =============================================================================== Job complete usr+sys time: 3401.74 seconds wall clock time: 61 minutes 16.68 seconds (3676.68 seconds total)