Starting phenix.real_space_refine on Fri Apr 5 19:59:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p73_17516/04_2024/8p73_17516_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 31 5.16 5 C 3292 2.51 5 N 870 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 262": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "I GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5169 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Unusual residues: {'ACE': 1} Classifications: {'peptide': 275, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'X50': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'X58': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C01AX50 J 401 " occ=0.29 ... (28 atoms not shown) pdb=" O28AX50 J 401 " occ=0.29 residue: pdb=" C01BX58 J 402 " occ=0.71 ... (28 atoms not shown) pdb=" O28BX58 J 402 " occ=0.71 Time building chain proxies: 3.31, per 1000 atoms: 0.64 Number of scatterers: 5169 At special positions: 0 Unit cell: (84.075, 93.3375, 67.6875, 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 31 16.00 O 976 8.00 N 870 7.00 C 3292 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 - 3.50 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: 2.20 Conformation dependent library (CDL) restraints added in 896.7 milliseconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 2 sheets defined 53.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.473A pdb=" N GLY H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 36 Processing helix chain 'I' and resid 50 through 70 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.511A pdb=" N LYS I 114 " --> pdb=" O PHE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 4.118A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.660A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.549A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 243 through 261 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 192 through 208 removed outlier: 4.195A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.738A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 215 hydrogen bonds defined for protein. 564 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: 1.31 Time building geometry restraints manager: 2.35 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: 1237 1.33 - 1.45: 1023 1.45 - 1.57: 2919 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5228 Sorted by residual: bond pdb=" C17AX50 J 401 " pdb=" C18AX50 J 401 " ideal model delta sigma weight residual 1.354 1.426 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C08AX50 J 401 " pdb=" N07AX50 J 401 " ideal model delta sigma weight residual 1.329 1.400 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C15AX50 J 401 " pdb=" C16AX50 J 401 " ideal model delta sigma weight residual 1.386 1.441 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" C02AX50 J 401 " pdb=" C04AX50 J 401 " ideal model delta sigma weight residual 1.588 1.533 0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C10BX58 J 402 " pdb=" C11BX58 J 402 " ideal model delta sigma weight residual 1.593 1.539 0.054 2.00e-02 2.50e+03 7.26e+00 ... (remaining 5223 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.19: 172 106.19 - 113.13: 2775 113.13 - 120.06: 1869 120.06 - 126.99: 2186 126.99 - 133.93: 77 Bond angle restraints: 7079 Sorted by residual: angle pdb=" CA LYS I 29 " pdb=" CB LYS I 29 " pdb=" CG LYS I 29 " ideal model delta sigma weight residual 114.10 122.63 -8.53 2.00e+00 2.50e-01 1.82e+01 angle pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " ideal model delta sigma weight residual 112.00 119.81 -7.81 2.20e+00 2.07e-01 1.26e+01 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 108.41 5.49 1.80e+00 3.09e-01 9.30e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.64e+00 angle pdb=" N07AX50 J 401 " pdb=" C08AX50 J 401 " pdb=" N09AX50 J 401 " ideal model delta sigma weight residual 110.97 119.07 -8.10 3.00e+00 1.11e-01 7.29e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.28: 2963 29.28 - 58.55: 153 58.55 - 87.83: 24 87.83 - 117.10: 4 117.10 - 146.38: 1 Dihedral angle restraints: 3145 sinusoidal: 1311 harmonic: 1834 Sorted by residual: dihedral pdb=" C08AX50 J 401 " pdb=" C10AX50 J 401 " pdb=" N09AX50 J 401 " pdb=" C11AX50 J 401 " ideal model delta sinusoidal sigma weight residual 199.01 52.63 146.38 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C23AX50 J 401 " pdb=" C24AX50 J 401 " pdb=" N25AX50 J 401 " pdb=" C26AX50 J 401 " ideal model delta sinusoidal sigma weight residual -52.89 62.46 -115.35 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C23BX58 J 402 " pdb=" C24BX58 J 402 " pdb=" N25BX58 J 402 " pdb=" C26BX58 J 402 " ideal model delta sinusoidal sigma weight residual 53.02 -59.35 112.37 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.987: 772 0.987 - 1.975: 0 1.975 - 2.962: 0 2.962 - 3.949: 0 3.949 - 4.936: 2 Chirality restraints: 774 Sorted by residual: chirality pdb=" C21BX58 J 402 " pdb=" C23BX58 J 402 " pdb=" C27BX58 J 402 " pdb=" O22BX58 J 402 " both_signs ideal model delta sigma weight residual False -2.47 2.47 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C21AX50 J 401 " pdb=" C23AX50 J 401 " pdb=" C27AX50 J 401 " pdb=" O22AX50 J 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.46 4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 771 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 279 " 0.258 9.50e-02 1.11e+02 1.16e-01 8.25e+00 pdb=" NE ARG I 279 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG I 279 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 279 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 279 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 116 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" CG ASP I 116 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP I 116 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP I 116 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO I 166 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.021 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 273 2.73 - 3.27: 5473 3.27 - 3.81: 9557 3.81 - 4.36: 11719 4.36 - 4.90: 18907 Nonbonded interactions: 45929 Sorted by model distance: nonbonded pdb=" OE1 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.182 2.440 nonbonded pdb=" OD1 ASP J 104 " pdb=" OG SER J 106 " model vdw 2.225 2.440 nonbonded pdb=" O HOH J 532 " pdb=" O HOH J 533 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR J 231 " pdb=" O LYS J 250 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP J 97 " pdb=" O HOH J 502 " model vdw 2.256 2.440 ... (remaining 45924 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=0.29 max=1.00 mean=0.99 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: 3.010 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: 12.560 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.010 Find NCS groups from input model: 0.160 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5228 Z= 0.322 Angle : 0.657 8.526 7079 Z= 0.317 Chirality : 0.254 4.936 774 Planarity : 0.006 0.116 898 Dihedral : 18.353 146.376 1957 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 1.45 % Allowed : 17.82 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.34), residues: 612 helix: 1.67 (0.28), residues: 334 sheet: 0.37 (1.51), residues: 15 loop : 0.15 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.015 0.002 PHE I 30 TYR 0.023 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.620 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 93 average time/residue: 1.4596 time to fit residues: 140.7002 Evaluate side-chains 92 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 274 LYS Chi-restraints excluded: chain J residue 242 SER Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5228 Z= 0.146 Angle : 0.903 26.623 7079 Z= 0.354 Chirality : 0.113 2.103 774 Planarity : 0.004 0.038 898 Dihedral : 10.830 146.638 722 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 1.82 % Allowed : 17.09 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.35), residues: 612 helix: 2.07 (0.30), residues: 328 sheet: 0.33 (1.47), residues: 15 loop : 0.31 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.013 0.001 PHE I 30 TYR 0.019 0.001 TYR I 91 ARG 0.002 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.565 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 94 average time/residue: 1.6391 time to fit residues: 160.1664 Evaluate side-chains 85 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5228 Z= 0.180 Angle : 0.888 25.724 7079 Z= 0.357 Chirality : 0.117 2.217 774 Planarity : 0.004 0.038 898 Dihedral : 9.728 147.771 708 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 1.09 % Allowed : 18.55 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.34), residues: 612 helix: 2.02 (0.29), residues: 328 sheet: 0.37 (1.48), residues: 15 loop : 0.31 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.013 0.002 PHE I 30 TYR 0.022 0.002 TYR I 91 ARG 0.003 0.000 ARG I 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: H 251 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.5232 (tp) REVERT: H 276 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5403 (ttt-90) outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 1.5341 time to fit residues: 139.8948 Evaluate side-chains 88 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 237 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5228 Z= 0.159 Angle : 0.878 25.589 7079 Z= 0.349 Chirality : 0.114 2.131 774 Planarity : 0.004 0.038 898 Dihedral : 9.726 145.178 708 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 1.64 % Allowed : 18.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.34), residues: 612 helix: 2.08 (0.29), residues: 328 sheet: 0.41 (1.49), residues: 15 loop : 0.33 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.012 0.002 PHE I 30 TYR 0.020 0.001 TYR I 91 ARG 0.002 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: H 276 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5405 (ttt-90) outliers start: 9 outliers final: 2 residues processed: 92 average time/residue: 1.5895 time to fit residues: 151.4098 Evaluate side-chains 87 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 237 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5228 Z= 0.324 Angle : 0.987 25.935 7079 Z= 0.414 Chirality : 0.119 2.213 774 Planarity : 0.006 0.040 898 Dihedral : 10.001 151.756 708 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 1.27 % Allowed : 18.18 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.33), residues: 612 helix: 1.48 (0.28), residues: 329 sheet: 0.36 (1.51), residues: 15 loop : 0.19 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP J 132 HIS 0.005 0.002 HIS J 135 PHE 0.017 0.003 PHE J 156 TYR 0.029 0.003 TYR I 91 ARG 0.006 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.658 Fit side-chains REVERT: H 276 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5443 (ttt-90) REVERT: I 250 ASP cc_start: 0.6200 (m-30) cc_final: 0.5883 (m-30) outliers start: 7 outliers final: 2 residues processed: 90 average time/residue: 1.6318 time to fit residues: 152.1173 Evaluate side-chains 90 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5228 Z= 0.244 Angle : 0.942 26.175 7079 Z= 0.386 Chirality : 0.117 2.206 774 Planarity : 0.005 0.036 898 Dihedral : 9.948 149.145 708 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 1.45 % Allowed : 18.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 612 helix: 1.64 (0.28), residues: 326 sheet: 0.48 (1.57), residues: 15 loop : 0.14 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.004 0.001 HIS J 258 PHE 0.015 0.002 PHE I 30 TYR 0.025 0.002 TYR I 91 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.626 Fit side-chains REVERT: H 276 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5626 (ttp-110) REVERT: I 250 ASP cc_start: 0.6189 (m-30) cc_final: 0.5871 (m-30) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 1.5407 time to fit residues: 142.0853 Evaluate side-chains 88 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 227 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.0418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5228 Z= 0.222 Angle : 0.926 26.028 7079 Z= 0.377 Chirality : 0.115 2.182 774 Planarity : 0.005 0.036 898 Dihedral : 9.873 148.205 708 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 0.91 % Allowed : 18.73 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.33), residues: 612 helix: 1.71 (0.28), residues: 328 sheet: 0.45 (1.56), residues: 15 loop : 0.09 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.023 0.002 TYR I 91 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.571 Fit side-chains REVERT: H 276 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5423 (ttt-90) outliers start: 5 outliers final: 3 residues processed: 87 average time/residue: 1.5387 time to fit residues: 138.6102 Evaluate side-chains 89 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 227 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 136 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5228 Z= 0.266 Angle : 0.958 26.128 7079 Z= 0.396 Chirality : 0.117 2.207 774 Planarity : 0.005 0.036 898 Dihedral : 9.927 149.557 708 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 1.27 % Allowed : 18.55 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.33), residues: 612 helix: 1.52 (0.28), residues: 328 sheet: 0.31 (1.51), residues: 15 loop : 0.11 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.004 0.001 HIS J 258 PHE 0.016 0.003 PHE I 30 TYR 0.026 0.002 TYR I 91 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.648 Fit side-chains REVERT: H 276 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5431 (ttt-90) REVERT: I 250 ASP cc_start: 0.6189 (m-30) cc_final: 0.5873 (m-30) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 1.5037 time to fit residues: 140.3359 Evaluate side-chains 92 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5228 Z= 0.184 Angle : 0.907 25.742 7079 Z= 0.367 Chirality : 0.113 2.148 774 Planarity : 0.005 0.038 898 Dihedral : 9.767 146.242 708 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 1.64 % Allowed : 18.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.34), residues: 612 helix: 1.86 (0.29), residues: 328 sheet: 0.39 (1.50), residues: 15 loop : 0.16 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.002 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.633 Fit side-chains REVERT: H 276 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5413 (ttt-90) REVERT: J 11 ARG cc_start: 0.5646 (ptt-90) cc_final: 0.5083 (ttt90) outliers start: 9 outliers final: 3 residues processed: 90 average time/residue: 1.4924 time to fit residues: 139.0515 Evaluate side-chains 88 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5228 Z= 0.288 Angle : 0.978 26.147 7079 Z= 0.406 Chirality : 0.117 2.210 774 Planarity : 0.005 0.035 898 Dihedral : 9.944 150.344 708 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 0.73 % Allowed : 19.27 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.33), residues: 612 helix: 1.54 (0.28), residues: 328 sheet: 0.36 (1.56), residues: 15 loop : 0.13 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.004 0.001 HIS J 258 PHE 0.015 0.003 PHE J 156 TYR 0.027 0.002 TYR I 91 ARG 0.005 0.001 ARG I 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.594 Fit side-chains REVERT: H 276 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5439 (ttt-90) REVERT: I 250 ASP cc_start: 0.6201 (m-30) cc_final: 0.5885 (m-30) outliers start: 4 outliers final: 3 residues processed: 88 average time/residue: 1.5015 time to fit residues: 136.8930 Evaluate side-chains 89 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155905 restraints weight = 10218.426| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.42 r_work: 0.3781 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5228 Z= 0.171 Angle : 0.900 25.604 7079 Z= 0.363 Chirality : 0.112 2.129 774 Planarity : 0.004 0.038 898 Dihedral : 9.745 145.193 708 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 0.73 % Allowed : 18.91 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.34), residues: 612 helix: 1.95 (0.29), residues: 328 sheet: 0.29 (1.45), residues: 15 loop : 0.20 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.019 0.001 TYR I 91 ARG 0.002 0.000 ARG I 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.33 seconds wall clock time: 54 minutes 51.12 seconds (3291.12 seconds total)