Starting phenix.real_space_refine on Wed Nov 13 23:22:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/11_2024/8ggt_40020.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/11_2024/8ggt_40020.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/8ggt_40020/11_2024/8ggt_40020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/11_2024/8ggt_40020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/11_2024/8ggt_40020.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/11_2024/8ggt_40020.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= 0.023 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 15 5.16 5 C 1405 2.51 5 N 335 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2105 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2090 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 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: 2.43, per 1000 atoms: 1.15 Number of scatterers: 2105 At special positions: 0 Unit cell: (56.4005, 84.1669, 61.6067, 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 15 16.00 O 350 8.00 N 335 7.00 C 1405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 0.54 Conformation dependent library (CDL) restraints added in 244.9 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: 12 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.787A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.580A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 5.254A 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 102 through 137 removed outlier: 3.739A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.722A pdb=" N LEU R 144 " --> pdb=" O LYS R 140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 140 through 145' Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.595A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix 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: 3.835A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.842A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.674A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.554A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.715A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 160 hydrogen bonds defined for protein. 480 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: 0.53 Time building geometry restraints manager: 0.63 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: 385 1.33 - 1.45: 561 1.45 - 1.57: 1190 1.57 - 1.69: 1 1.69 - 1.81: 22 Bond restraints: 2159 Sorted by residual: bond pdb=" C LEU R 287 " pdb=" O LEU R 287 " ideal model delta sigma weight residual 1.244 1.211 0.032 9.80e-03 1.04e+04 1.09e+01 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 7.10e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.576 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.28e+00 ... (remaining 2154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 2914 2.19 - 4.39: 34 4.39 - 6.58: 8 6.58 - 8.77: 4 8.77 - 10.96: 1 Bond angle restraints: 2961 Sorted by residual: angle pdb=" N PHE R 289 " pdb=" CA PHE R 289 " pdb=" C PHE R 289 " ideal model delta sigma weight residual 111.07 118.45 -7.38 1.07e+00 8.73e-01 4.75e+01 angle pdb=" N TRP R 286 " pdb=" CA TRP R 286 " pdb=" C TRP R 286 " ideal model delta sigma weight residual 113.97 121.51 -7.54 1.28e+00 6.10e-01 3.47e+01 angle pdb=" CA MET R 36 " pdb=" CB MET R 36 " pdb=" CG MET R 36 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CB MET R 36 " pdb=" CG MET R 36 " pdb=" SD MET R 36 " ideal model delta sigma weight residual 112.70 123.66 -10.96 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C LEU R 287 " pdb=" N PRO R 288 " pdb=" CA PRO R 288 " ideal model delta sigma weight residual 119.05 115.01 4.04 1.11e+00 8.12e-01 1.32e+01 ... (remaining 2956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1124 16.67 - 33.33: 81 33.33 - 49.99: 25 49.99 - 66.66: 2 66.66 - 83.32: 3 Dihedral angle restraints: 1235 sinusoidal: 407 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -169.32 83.32 1 1.00e+01 1.00e-02 8.48e+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 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+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 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 254 0.042 - 0.083: 90 0.083 - 0.124: 18 0.124 - 0.165: 0 0.165 - 0.207: 2 Chirality restraints: 364 Sorted by residual: 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 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 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 2.57 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA PHE R 289 " pdb=" N PHE R 289 " pdb=" C PHE R 289 " pdb=" CB PHE R 289 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 361 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 36 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C MET R 36 " 0.035 2.00e-02 2.50e+03 pdb=" O MET R 36 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY R 37 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 287 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO R 288 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C THR R 281 " 0.026 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.009 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 408 2.77 - 3.30: 2079 3.30 - 3.84: 3341 3.84 - 4.37: 3350 4.37 - 4.90: 6282 Nonbonded interactions: 15460 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.240 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.307 3.040 nonbonded pdb=" NE1 TRP R 99 " pdb=" O GLY R 102 " model vdw 2.504 3.120 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.527 3.040 nonbonded pdb=" OG SER R 165 " pdb=" N PHE R 166 " model vdw 2.531 3.120 ... (remaining 15455 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=0.00 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: 1.480 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.270 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 2159 Z= 0.294 Angle : 0.700 10.965 2961 Z= 0.420 Chirality : 0.041 0.207 364 Planarity : 0.004 0.039 358 Dihedral : 13.407 78.387 694 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.49), residues: 277 helix: 2.41 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.50 (0.55), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.002 0.001 HIS R 178 PHE 0.012 0.001 PHE R 139 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** 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 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1444 time to fit residues: 3.8061 Evaluate side-chains 16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.0050 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2159 Z= 0.169 Angle : 0.490 6.438 2961 Z= 0.278 Chirality : 0.039 0.156 364 Planarity : 0.004 0.032 358 Dihedral : 4.430 17.988 311 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.00 % Allowed : 5.50 % Favored : 92.50 % 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: 2.27 (0.50), residues: 277 helix: 2.64 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.42 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 328 *********************** 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 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7389 (mtt) cc_final: 0.7108 (mtt) outliers start: 4 outliers final: 4 residues processed: 19 average time/residue: 0.1396 time to fit residues: 3.4070 Evaluate side-chains 20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 309 ILE 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: 1.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2159 Z= 0.207 Angle : 0.502 5.971 2961 Z= 0.282 Chirality : 0.040 0.136 364 Planarity : 0.004 0.026 358 Dihedral : 4.463 17.784 311 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.00 % Allowed : 7.50 % Favored : 90.50 % 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: 2.28 (0.51), residues: 277 helix: 2.62 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.32 (0.66), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7541 (mtt) cc_final: 0.7246 (mtt) outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.1321 time to fit residues: 3.3791 Evaluate side-chains 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2159 Z= 0.131 Angle : 0.456 7.360 2961 Z= 0.252 Chirality : 0.038 0.133 364 Planarity : 0.003 0.025 358 Dihedral : 4.225 17.799 311 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.00 % Allowed : 10.50 % Favored : 88.50 % 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: 2.57 (0.52), residues: 277 helix: 2.88 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.31 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 286 HIS 0.002 0.001 HIS R 178 PHE 0.007 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 20 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7425 (mtt) cc_final: 0.7119 (mtt) REVERT: R 156 MET cc_start: 0.6903 (mmt) cc_final: 0.6391 (mmt) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1430 time to fit residues: 3.5974 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2159 Z= 0.227 Angle : 0.519 7.676 2961 Z= 0.285 Chirality : 0.040 0.127 364 Planarity : 0.004 0.026 358 Dihedral : 4.371 17.542 311 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 11.50 % Favored : 85.50 % 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: 2.35 (0.52), residues: 277 helix: 2.70 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.34 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7510 (mtt) cc_final: 0.7209 (mtt) REVERT: R 95 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 6 outliers final: 4 residues processed: 23 average time/residue: 0.1686 time to fit residues: 4.6477 Evaluate side-chains 22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2159 Z= 0.175 Angle : 0.494 8.947 2961 Z= 0.269 Chirality : 0.039 0.127 364 Planarity : 0.003 0.026 358 Dihedral : 4.297 17.559 311 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 13.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.51), residues: 277 helix: 2.78 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.32 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** 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 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7492 (mtt) cc_final: 0.7187 (mtt) REVERT: R 95 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (mp) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.0830 time to fit residues: 2.3978 Evaluate side-chains 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2159 Z= 0.144 Angle : 0.469 9.227 2961 Z= 0.253 Chirality : 0.038 0.122 364 Planarity : 0.003 0.025 358 Dihedral : 4.124 17.436 311 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.00 % Allowed : 13.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.51), residues: 277 helix: 3.04 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.36 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 178 PHE 0.006 0.001 PHE R 61 TYR 0.010 0.001 TYR R 185 ARG 0.001 0.000 ARG R 151 *********************** 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 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7381 (mtt) cc_final: 0.7069 (mtt) REVERT: R 95 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8449 (mp) REVERT: R 133 PHE cc_start: 0.8113 (m-80) cc_final: 0.7732 (t80) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.0929 time to fit residues: 2.6326 Evaluate side-chains 21 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2159 Z= 0.181 Angle : 0.509 10.229 2961 Z= 0.274 Chirality : 0.039 0.120 364 Planarity : 0.003 0.025 358 Dihedral : 4.196 17.261 311 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.00 % Allowed : 12.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.52), residues: 277 helix: 2.85 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.30 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7500 (mtt) cc_final: 0.7182 (mtt) REVERT: R 95 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8429 (mp) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.1746 time to fit residues: 4.8306 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2159 Z= 0.185 Angle : 0.511 10.828 2961 Z= 0.274 Chirality : 0.039 0.123 364 Planarity : 0.004 0.026 358 Dihedral : 4.202 17.409 311 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.00 % Allowed : 12.50 % Favored : 84.50 % 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: 2.51 (0.52), residues: 277 helix: 2.82 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.27 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 286 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7532 (mtt) cc_final: 0.7220 (mtt) REVERT: R 95 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8469 (mp) outliers start: 6 outliers final: 5 residues processed: 21 average time/residue: 0.0892 time to fit residues: 2.6664 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2159 Z= 0.194 Angle : 0.524 10.968 2961 Z= 0.281 Chirality : 0.039 0.123 364 Planarity : 0.004 0.026 358 Dihedral : 4.240 17.411 311 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.00 % Allowed : 13.50 % Favored : 83.50 % 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: 2.48 (0.52), residues: 277 helix: 2.79 (0.34), residues: 208 sheet: None (None), residues: 0 loop : -2.25 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 ********************** 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 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7565 (mtt) cc_final: 0.7266 (mtt) REVERT: R 95 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8479 (mp) outliers start: 6 outliers final: 5 residues processed: 21 average time/residue: 0.0846 time to fit residues: 2.5191 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127934 restraints weight = 3137.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130712 restraints weight = 1724.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132483 restraints weight = 1133.486| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2159 Z= 0.195 Angle : 0.524 10.989 2961 Z= 0.281 Chirality : 0.039 0.123 364 Planarity : 0.004 0.026 358 Dihedral : 4.242 17.418 311 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 13.50 % Favored : 83.50 % 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: 2.47 (0.52), residues: 277 helix: 2.78 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -2.22 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 940.24 seconds wall clock time: 17 minutes 53.22 seconds (1073.22 seconds total)