Starting phenix.real_space_refine on Mon Sep 23 20:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/09_2024/7yi8_33853.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3334 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.72, per 1000 atoms: 0.71 Number of scatterers: 5225 At special positions: 0 Unit cell: (70.55, 73.1, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 972 8.00 N 892 7.00 C 3334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.32 Conformation dependent library (CDL) restraints added in 599.6 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 39.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.965A pdb=" N ASN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.275A pdb=" N SER A 340 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 402 through 414 removed outlier: 3.721A pdb=" N LEU A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 418 removed outlier: 3.618A pdb=" N GLN A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'B' and resid 141 through 165 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.690A pdb=" N GLN B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.752A pdb=" N GLN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.910A pdb=" N LEU C 167 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 183 removed outlier: 4.377A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.567A pdb=" N TYR D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 19 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.693A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.214A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 removed outlier: 4.309A pdb=" N ILE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.637A pdb=" N ASN D 128 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.619A pdb=" N LYS A 125 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 447 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 127 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A 145 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 183 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 187 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS A 360 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER A 212 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 362 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN A 210 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 364 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 176 through 180 removed outlier: 4.061A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 300 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 277 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS B 302 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU B 275 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 504 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: 1.20 Time building geometry restraints manager: 1.54 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: 1406 1.33 - 1.45: 870 1.45 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5318 Sorted by residual: bond pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C8 SAH B 401 " pdb=" N7 SAH B 401 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C2 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C6 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1' SAH B 401 " pdb=" N9 SAH B 401 " ideal model delta sigma weight residual 1.440 1.476 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 5313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 7036 2.07 - 4.14: 96 4.14 - 6.21: 10 6.21 - 8.27: 2 8.27 - 10.34: 3 Bond angle restraints: 7147 Sorted by residual: angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 91.43 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O SAH B 401 " pdb=" C SAH B 401 " pdb=" OXT SAH B 401 " ideal model delta sigma weight residual 126.79 117.95 8.84 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C LYS B 317 " pdb=" N ASN B 318 " pdb=" CA ASN B 318 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " pdb=" C4 SAH B 401 " ideal model delta sigma weight residual 111.67 120.13 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N1 SAH B 401 " pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 128.45 120.52 7.93 3.00e+00 1.11e-01 6.99e+00 ... (remaining 7142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 2895 17.61 - 35.23: 266 35.23 - 52.84: 60 52.84 - 70.45: 10 70.45 - 88.07: 6 Dihedral angle restraints: 3237 sinusoidal: 1382 harmonic: 1855 Sorted by residual: dihedral pdb=" CA MET A 401 " pdb=" C MET A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " ideal model delta sinusoidal sigma weight residual -90.00 -134.61 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 201 " pdb=" CG GLU A 201 " pdb=" CD GLU A 201 " pdb=" OE1 GLU A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -88.07 88.07 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 489 0.034 - 0.068: 212 0.068 - 0.102: 50 0.102 - 0.136: 26 0.136 - 0.170: 3 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA GLN B 155 " pdb=" N GLN B 155 " pdb=" C GLN B 155 " pdb=" CB GLN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 777 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 151 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C LEU B 151 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 151 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO A 353 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 51 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 52 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " 0.023 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 200 2.72 - 3.27: 5149 3.27 - 3.81: 8125 3.81 - 4.36: 10477 4.36 - 4.90: 17641 Nonbonded interactions: 41592 Sorted by model distance: nonbonded pdb=" OG SER B 326 " pdb=" OE2 GLU B 337 " model vdw 2.179 3.040 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 261 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 383 " pdb=" NZ LYS B 289 " model vdw 2.257 3.120 nonbonded pdb=" O CYS B 346 " pdb=" OH TYR B 351 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 407 " pdb=" OE1 GLU A 431 " model vdw 2.286 3.040 ... (remaining 41587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5318 Z= 0.188 Angle : 0.608 10.344 7147 Z= 0.301 Chirality : 0.043 0.170 780 Planarity : 0.004 0.047 909 Dihedral : 14.732 88.067 2031 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 620 helix: 0.07 (0.37), residues: 193 sheet: -0.33 (0.47), residues: 104 loop : -0.51 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 107 HIS 0.003 0.001 HIS B 152 PHE 0.012 0.001 PHE A 355 TYR 0.013 0.001 TYR A 352 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.615 Fit side-chains REVERT: A 384 ASP cc_start: 0.7231 (t70) cc_final: 0.6985 (t0) REVERT: A 405 TYR cc_start: 0.7434 (t80) cc_final: 0.7153 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.1616 time to fit residues: 149.1175 Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 83 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5318 Z= 0.322 Angle : 0.663 7.305 7147 Z= 0.345 Chirality : 0.045 0.160 780 Planarity : 0.005 0.069 909 Dihedral : 5.563 55.503 676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 14.04 % Favored : 82.84 % 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: -0.86 (0.33), residues: 620 helix: -0.48 (0.35), residues: 209 sheet: -0.13 (0.48), residues: 103 loop : -0.68 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 252 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.002 PHE B 293 TYR 0.019 0.002 TYR A 207 ARG 0.007 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: B 353 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: D 108 ILE cc_start: 0.7087 (mp) cc_final: 0.6690 (mt) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 1.2955 time to fit residues: 125.9058 Evaluate side-chains 81 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 380 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5318 Z= 0.193 Angle : 0.548 6.008 7147 Z= 0.287 Chirality : 0.041 0.149 780 Planarity : 0.004 0.057 909 Dihedral : 5.142 50.773 676 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.77 % Allowed : 16.98 % Favored : 80.24 % 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: -0.72 (0.33), residues: 620 helix: -0.17 (0.36), residues: 211 sheet: -0.09 (0.52), residues: 93 loop : -0.72 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 PHE 0.009 0.001 PHE B 158 TYR 0.019 0.001 TYR A 207 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.962 Fit side-chains REVERT: B 353 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7279 (tt0) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 1.0340 time to fit residues: 90.8513 Evaluate side-chains 78 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5318 Z= 0.213 Angle : 0.562 6.525 7147 Z= 0.291 Chirality : 0.041 0.147 780 Planarity : 0.004 0.056 909 Dihedral : 5.114 49.810 676 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.33 % Allowed : 16.98 % Favored : 78.68 % 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: -0.76 (0.33), residues: 620 helix: -0.14 (0.35), residues: 211 sheet: -0.11 (0.52), residues: 93 loop : -0.81 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.001 HIS D 39 PHE 0.012 0.002 PHE B 203 TYR 0.017 0.002 TYR A 207 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.652 Fit side-chains REVERT: A 173 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6953 (mmtm) REVERT: B 353 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: D 86 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7165 (mm-30) outliers start: 25 outliers final: 15 residues processed: 83 average time/residue: 1.0149 time to fit residues: 88.6929 Evaluate side-chains 85 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 86 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5318 Z= 0.185 Angle : 0.544 6.662 7147 Z= 0.281 Chirality : 0.041 0.141 780 Planarity : 0.004 0.054 909 Dihedral : 4.951 48.161 676 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.99 % Allowed : 18.02 % Favored : 77.99 % 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: -0.69 (0.33), residues: 620 helix: -0.02 (0.36), residues: 211 sheet: -0.01 (0.53), residues: 93 loop : -0.83 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 365 HIS 0.002 0.001 HIS C 169 PHE 0.011 0.001 PHE B 158 TYR 0.016 0.001 TYR A 207 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6962 (mmtm) REVERT: B 353 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: D 86 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6846 (mm-30) outliers start: 23 outliers final: 13 residues processed: 87 average time/residue: 1.0166 time to fit residues: 93.0796 Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 86 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.0000 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5318 Z= 0.237 Angle : 0.593 6.981 7147 Z= 0.305 Chirality : 0.042 0.146 780 Planarity : 0.004 0.056 909 Dihedral : 5.049 45.623 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.68 % Allowed : 18.89 % Favored : 76.43 % 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: -0.77 (0.33), residues: 620 helix: -0.09 (0.36), residues: 211 sheet: -0.06 (0.54), residues: 93 loop : -0.88 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 365 HIS 0.002 0.001 HIS D 39 PHE 0.012 0.002 PHE B 203 TYR 0.017 0.002 TYR A 352 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6977 (mmtm) REVERT: B 353 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7201 (tt0) outliers start: 27 outliers final: 14 residues processed: 96 average time/residue: 1.0841 time to fit residues: 109.3647 Evaluate side-chains 90 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5318 Z= 0.155 Angle : 0.539 7.162 7147 Z= 0.277 Chirality : 0.040 0.133 780 Planarity : 0.004 0.053 909 Dihedral : 4.750 47.349 676 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.64 % Allowed : 20.80 % Favored : 75.56 % 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: -0.63 (0.33), residues: 620 helix: 0.10 (0.37), residues: 210 sheet: 0.02 (0.54), residues: 94 loop : -0.85 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 365 HIS 0.001 0.000 HIS D 39 PHE 0.011 0.001 PHE B 203 TYR 0.017 0.001 TYR A 207 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6929 (mmtm) REVERT: D 21 MET cc_start: 0.7796 (mmm) cc_final: 0.7564 (mmm) outliers start: 21 outliers final: 10 residues processed: 93 average time/residue: 1.0119 time to fit residues: 98.8049 Evaluate side-chains 81 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5318 Z= 0.188 Angle : 0.569 8.271 7147 Z= 0.291 Chirality : 0.041 0.137 780 Planarity : 0.005 0.083 909 Dihedral : 4.802 47.525 676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.77 % Allowed : 22.01 % Favored : 75.22 % 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: -0.63 (0.33), residues: 620 helix: 0.11 (0.37), residues: 210 sheet: 0.07 (0.54), residues: 93 loop : -0.87 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 PHE 0.010 0.001 PHE B 203 TYR 0.015 0.001 TYR A 207 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.628 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.9686 time to fit residues: 88.0974 Evaluate side-chains 83 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5318 Z= 0.165 Angle : 0.553 8.648 7147 Z= 0.280 Chirality : 0.041 0.169 780 Planarity : 0.005 0.081 909 Dihedral : 4.713 48.406 676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.60 % Allowed : 22.18 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.33), residues: 620 helix: 0.16 (0.37), residues: 210 sheet: 0.05 (0.54), residues: 93 loop : -0.89 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 365 HIS 0.001 0.000 HIS D 39 PHE 0.011 0.001 PHE B 203 TYR 0.016 0.001 TYR A 207 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6840 (mp0) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.9569 time to fit residues: 87.2793 Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5318 Z= 0.210 Angle : 0.607 9.497 7147 Z= 0.308 Chirality : 0.042 0.176 780 Planarity : 0.005 0.089 909 Dihedral : 4.836 47.723 676 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.43 % Allowed : 23.05 % Favored : 74.52 % 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: -0.70 (0.33), residues: 620 helix: 0.13 (0.37), residues: 209 sheet: -0.01 (0.54), residues: 93 loop : -0.96 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 365 HIS 0.002 0.001 HIS D 39 PHE 0.012 0.001 PHE B 203 TYR 0.016 0.001 TYR A 352 ARG 0.005 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 401 MET cc_start: 0.6596 (mmt) cc_final: 0.6308 (tpt) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.9032 time to fit residues: 80.3339 Evaluate side-chains 83 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 226 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.191125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156793 restraints weight = 6034.529| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.68 r_work: 0.3778 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5318 Z= 0.140 Angle : 0.529 7.959 7147 Z= 0.270 Chirality : 0.040 0.142 780 Planarity : 0.004 0.069 909 Dihedral : 4.558 52.022 676 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.25 % Allowed : 23.40 % Favored : 74.35 % 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: -0.62 (0.33), residues: 620 helix: 0.27 (0.37), residues: 211 sheet: -0.17 (0.56), residues: 88 loop : -0.91 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 365 HIS 0.001 0.000 HIS C 169 PHE 0.009 0.001 PHE B 203 TYR 0.019 0.001 TYR A 207 ARG 0.004 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.57 seconds wall clock time: 44 minutes 15.95 seconds (2655.95 seconds total)