Starting phenix.real_space_refine on Wed Nov 13 23:14:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggv_40022/11_2024/8ggv_40022.cif" } resolution = 3.5 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= 0.021 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 13 5.16 5 C 1378 2.51 5 N 331 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2049 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 1.40 Number of scatterers: 2064 At special positions: 0 Unit cell: (55.5328, 82.4315, 62.4744, 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 13 16.00 O 342 8.00 N 331 7.00 C 1378 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: 0.57 Conformation dependent library (CDL) restraints added in 291.2 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.634A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.105A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.928A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.603A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.807A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.950A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.974A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.720A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 165 hydrogen bonds defined for protein. 495 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: 0.51 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 628 1.34 - 1.46: 449 1.46 - 1.57: 1022 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2117 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.321 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 2112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 2736 1.09 - 2.19: 136 2.19 - 3.28: 22 3.28 - 4.38: 8 4.38 - 5.47: 5 Bond angle restraints: 2907 Sorted by residual: angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.03e+00 angle pdb=" C LEU R 95 " pdb=" N THR R 96 " pdb=" CA THR R 96 " ideal model delta sigma weight residual 122.06 118.50 3.56 1.86e+00 2.89e-01 3.65e+00 angle pdb=" C ILE R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 120.42 117.77 2.65 1.42e+00 4.96e-01 3.47e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.10 -5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.25 3.21 1.80e+00 3.09e-01 3.17e+00 ... (remaining 2902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 1087 15.90 - 31.79: 88 31.79 - 47.69: 25 47.69 - 63.59: 2 63.59 - 79.48: 2 Dihedral angle restraints: 1204 sinusoidal: 376 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 170 " pdb=" C GLN R 170 " pdb=" N MET R 171 " pdb=" CA MET R 171 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 1201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 223 0.033 - 0.066: 96 0.066 - 0.099: 34 0.099 - 0.131: 2 0.131 - 0.164: 1 Chirality restraints: 356 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.78e-01 chirality pdb=" CA LEU R 167 " pdb=" N LEU R 167 " pdb=" C LEU R 167 " pdb=" CB LEU R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.58e-01 ... (remaining 353 not shown) Planarity restraints: 355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO R 168 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ILE R 277 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO R 211 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.015 5.00e-02 4.00e+02 ... (remaining 352 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 504 2.80 - 3.33: 2090 3.33 - 3.85: 3338 3.85 - 4.38: 3268 4.38 - 4.90: 5978 Nonbonded interactions: 15178 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.276 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.529 3.040 nonbonded pdb=" OE1 GLU R 62 " pdb=" NH1 ARG R 63 " model vdw 2.546 3.120 nonbonded pdb=" NE1 TRP R 99 " pdb=" O GLY R 102 " model vdw 2.585 3.120 ... (remaining 15173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2117 Z= 0.241 Angle : 0.593 5.473 2907 Z= 0.326 Chirality : 0.039 0.164 356 Planarity : 0.003 0.036 355 Dihedral : 13.635 79.481 666 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.50), residues: 277 helix: 2.36 (0.34), residues: 216 sheet: None (None), residues: 0 loop : -2.56 (0.66), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.014 0.002 PHE R 336 TYR 0.005 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1039 time to fit residues: 5.6729 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2117 Z= 0.164 Angle : 0.500 5.009 2907 Z= 0.274 Chirality : 0.039 0.124 356 Planarity : 0.003 0.026 355 Dihedral : 4.817 18.374 311 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.16 % Allowed : 12.97 % Favored : 84.86 % 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: 2.44 (0.50), residues: 277 helix: 2.56 (0.33), residues: 218 sheet: None (None), residues: 0 loop : -2.27 (0.69), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 166 TYR 0.007 0.001 TYR R 326 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.188 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.0970 time to fit residues: 4.8883 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2117 Z= 0.237 Angle : 0.533 5.125 2907 Z= 0.292 Chirality : 0.039 0.120 356 Planarity : 0.003 0.027 355 Dihedral : 4.788 20.235 311 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.41 % Allowed : 15.68 % Favored : 78.92 % 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: 2.49 (0.51), residues: 277 helix: 2.61 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.62 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.009 0.001 TYR R 326 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.235 Fit side-chains REVERT: R 309 ILE cc_start: 0.8791 (mm) cc_final: 0.8233 (pt) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.0983 time to fit residues: 4.9520 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2117 Z= 0.201 Angle : 0.510 5.824 2907 Z= 0.276 Chirality : 0.039 0.119 356 Planarity : 0.003 0.027 355 Dihedral : 4.672 19.843 311 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 8.11 % Allowed : 15.68 % Favored : 76.22 % 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: 2.50 (0.50), residues: 277 helix: 2.63 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.68 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.009 0.001 TYR R 185 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.230 Fit side-chains REVERT: R 309 ILE cc_start: 0.8797 (mm) cc_final: 0.8159 (pt) outliers start: 15 outliers final: 13 residues processed: 41 average time/residue: 0.0926 time to fit residues: 4.8328 Evaluate side-chains 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 332 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2117 Z= 0.158 Angle : 0.474 5.518 2907 Z= 0.256 Chirality : 0.038 0.115 356 Planarity : 0.003 0.026 355 Dihedral : 4.427 18.283 311 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.95 % Allowed : 19.46 % Favored : 74.59 % 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: 2.62 (0.51), residues: 277 helix: 2.78 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.73 (0.69), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 326 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.227 Fit side-chains REVERT: R 309 ILE cc_start: 0.8804 (mm) cc_final: 0.8185 (pt) outliers start: 11 outliers final: 8 residues processed: 42 average time/residue: 0.1005 time to fit residues: 5.3694 Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 332 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2117 Z= 0.140 Angle : 0.459 5.776 2907 Z= 0.246 Chirality : 0.037 0.111 356 Planarity : 0.003 0.024 355 Dihedral : 4.253 17.799 311 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.95 % Allowed : 21.08 % Favored : 72.97 % 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: 2.75 (0.51), residues: 277 helix: 2.83 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -2.61 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 282 TYR 0.005 0.001 TYR R 326 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.222 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 42 average time/residue: 0.0956 time to fit residues: 5.1937 Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2117 Z= 0.143 Angle : 0.464 6.752 2907 Z= 0.247 Chirality : 0.037 0.110 356 Planarity : 0.003 0.024 355 Dihedral : 4.222 17.691 311 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.86 % Allowed : 22.70 % Favored : 72.43 % 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: 2.90 (0.51), residues: 277 helix: 2.93 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.59 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.005 0.001 TYR R 326 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.237 Fit side-chains REVERT: R 318 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8231 (t0) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.0916 time to fit residues: 4.4580 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 318 ASN Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2117 Z= 0.191 Angle : 0.510 7.615 2907 Z= 0.265 Chirality : 0.038 0.121 356 Planarity : 0.003 0.024 355 Dihedral : 4.326 17.711 311 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.41 % Allowed : 22.70 % Favored : 71.89 % 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: 2.77 (0.51), residues: 277 helix: 2.84 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.66 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.005 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.226 Fit side-chains REVERT: R 318 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7490 (m-40) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.1010 time to fit residues: 4.9778 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 318 ASN Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2117 Z= 0.204 Angle : 0.518 8.066 2907 Z= 0.272 Chirality : 0.038 0.112 356 Planarity : 0.003 0.025 355 Dihedral : 4.419 18.049 311 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.86 % Allowed : 24.32 % Favored : 70.81 % 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: 2.66 (0.51), residues: 277 helix: 2.76 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.67 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.212 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.0943 time to fit residues: 4.5934 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2117 Z= 0.163 Angle : 0.513 8.449 2907 Z= 0.267 Chirality : 0.038 0.114 356 Planarity : 0.003 0.024 355 Dihedral : 4.347 17.765 311 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.32 % Allowed : 24.32 % Favored : 71.35 % 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: 2.72 (0.51), residues: 277 helix: 2.78 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.56 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.004 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.209 Fit side-chains REVERT: R 156 MET cc_start: 0.7479 (tmm) cc_final: 0.7236 (tmm) outliers start: 8 outliers final: 8 residues processed: 38 average time/residue: 0.0947 time to fit residues: 4.6382 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129167 restraints weight = 3275.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132044 restraints weight = 1635.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134246 restraints weight = 1009.506| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2117 Z= 0.218 Angle : 0.545 8.516 2907 Z= 0.287 Chirality : 0.039 0.115 356 Planarity : 0.003 0.025 355 Dihedral : 4.502 18.665 311 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.86 % Allowed : 23.78 % Favored : 71.35 % 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: 2.66 (0.51), residues: 277 helix: 2.75 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.65 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 892.86 seconds wall clock time: 21 minutes 47.52 seconds (1307.52 seconds total)