Starting phenix.real_space_refine on Wed Nov 13 23:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggo_40015/11_2024/8ggo_40015.cif" } resolution = 3.2 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= 0.028 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 1403 2.51 5 N 330 2.21 5 O 349 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: 2095 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2080 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 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: 2.61, per 1000 atoms: 1.25 Number of scatterers: 2095 At special positions: 0 Unit cell: (56.4005, 82.4315, 64.2098, 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 349 8.00 N 330 7.00 C 1403 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=2.04 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 292.1 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 534 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.566A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 66 removed outlier: 3.587A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR R 66 " --> pdb=" O ARG R 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 66' Processing helix chain 'R' and resid 67 through 86 removed outlier: 4.311A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 removed outlier: 3.534A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.690A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.844A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.925A 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 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.741A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.524A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.627A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.819A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.805A 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 removed outlier: 3.649A pdb=" N GLU R 338 " --> pdb=" O ILE R 334 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 340 " --> pdb=" O PHE R 336 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 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: 0.55 Time building geometry restraints manager: 0.62 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: 359 1.33 - 1.45: 594 1.45 - 1.57: 1180 1.57 - 1.69: 1 1.69 - 1.81: 17 Bond restraints: 2151 Sorted by residual: bond pdb=" C ARG R 328 " pdb=" N SER R 329 " ideal model delta sigma weight residual 1.331 1.250 0.081 2.07e-02 2.33e+03 1.51e+01 bond pdb=" C CYS R 327 " pdb=" N ARG R 328 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.37e-02 5.33e+03 1.23e+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 6.96e+00 bond pdb=" CA VAL R 86 " pdb=" C VAL R 86 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.37e-02 5.33e+03 6.77e+00 bond pdb=" CA VAL R 81 " pdb=" C VAL R 81 " ideal model delta sigma weight residual 1.523 1.493 0.031 1.27e-02 6.20e+03 5.77e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2879 1.85 - 3.71: 55 3.71 - 5.56: 16 5.56 - 7.42: 5 7.42 - 9.27: 2 Bond angle restraints: 2957 Sorted by residual: angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 111.36 118.41 -7.05 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N ALA R 85 " pdb=" CA ALA R 85 " pdb=" C ALA R 85 " ideal model delta sigma weight residual 113.97 122.12 -8.15 1.28e+00 6.10e-01 4.05e+01 angle pdb=" N CYS R 327 " pdb=" CA CYS R 327 " pdb=" C CYS R 327 " ideal model delta sigma weight residual 111.07 116.65 -5.58 1.07e+00 8.73e-01 2.72e+01 angle pdb=" N TYR R 326 " pdb=" CA TYR R 326 " pdb=" C TYR R 326 " ideal model delta sigma weight residual 111.69 118.05 -6.36 1.23e+00 6.61e-01 2.67e+01 angle pdb=" C VAL R 87 " pdb=" N PRO R 88 " pdb=" CA PRO R 88 " ideal model delta sigma weight residual 119.05 113.44 5.61 1.11e+00 8.12e-01 2.55e+01 ... (remaining 2952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 1102 14.89 - 29.77: 89 29.77 - 44.65: 25 44.65 - 59.53: 2 59.53 - 74.41: 1 Dihedral angle restraints: 1219 sinusoidal: 397 harmonic: 822 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 -160.41 74.41 1 1.00e+01 1.00e-02 7.02e+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 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA SER R 207 " pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 280 0.048 - 0.096: 71 0.096 - 0.144: 11 0.144 - 0.191: 4 0.191 - 0.239: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" CA ALA R 85 " pdb=" N ALA R 85 " pdb=" C ALA R 85 " pdb=" CB ALA R 85 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA PHE R 89 " pdb=" N PHE R 89 " pdb=" C PHE R 89 " pdb=" CB PHE R 89 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA CYS R 327 " pdb=" N CYS R 327 " pdb=" C CYS R 327 " pdb=" CB CYS R 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 365 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 327 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C CYS R 327 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS R 327 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG R 328 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 79 " 0.009 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ASP R 79 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP R 79 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU R 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 328 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C ARG R 328 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG R 328 " -0.009 2.00e-02 2.50e+03 pdb=" N SER R 329 " -0.008 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 610 2.83 - 3.34: 2140 3.34 - 3.86: 3322 3.86 - 4.38: 3474 4.38 - 4.90: 6381 Nonbonded interactions: 15927 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.307 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.452 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.489 3.040 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.532 3.040 ... (remaining 15922 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.910 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 2151 Z= 0.360 Angle : 0.737 9.272 2957 Z= 0.481 Chirality : 0.046 0.239 368 Planarity : 0.004 0.030 354 Dihedral : 11.582 49.341 682 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 2.30 (0.50), residues: 275 helix: 2.14 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -0.93 (0.81), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 89 TYR 0.010 0.001 TYR R 132 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1406 time to fit residues: 2.4255 Evaluate side-chains 11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.204 Angle : 0.493 5.213 2957 Z= 0.278 Chirality : 0.040 0.116 368 Planarity : 0.004 0.027 354 Dihedral : 4.628 19.872 308 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.97 % Allowed : 2.96 % Favored : 95.07 % 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: 2.41 (0.51), residues: 275 helix: 2.21 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.13 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE R 108 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.320 Fit side-chains REVERT: R 82 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7305 (mtm) outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.0684 time to fit residues: 1.7702 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2151 Z= 0.204 Angle : 0.481 5.257 2957 Z= 0.271 Chirality : 0.039 0.117 368 Planarity : 0.003 0.026 354 Dihedral : 4.437 19.890 308 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.48 % Allowed : 5.42 % Favored : 93.10 % 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: 2.45 (0.51), residues: 275 helix: 2.22 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.01 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 101 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.233 Fit side-chains REVERT: R 82 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7397 (mtm) outliers start: 3 outliers final: 1 residues processed: 14 average time/residue: 0.0763 time to fit residues: 1.6744 Evaluate side-chains 12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2151 Z= 0.192 Angle : 0.463 5.246 2957 Z= 0.262 Chirality : 0.039 0.115 368 Planarity : 0.003 0.027 354 Dihedral : 4.368 20.673 308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.46 % Allowed : 8.37 % Favored : 89.16 % 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: 2.56 (0.52), residues: 275 helix: 2.29 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -0.93 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.185 Fit side-chains REVERT: R 82 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (mtm) outliers start: 5 outliers final: 1 residues processed: 15 average time/residue: 0.0579 time to fit residues: 1.3983 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 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: 0.8089 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2151 Z= 0.200 Angle : 0.462 5.266 2957 Z= 0.261 Chirality : 0.039 0.113 368 Planarity : 0.003 0.027 354 Dihedral : 4.331 20.616 308 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 10.34 % Favored : 88.18 % 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: 2.52 (0.52), residues: 275 helix: 2.27 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.01 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.209 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 13 average time/residue: 0.0721 time to fit residues: 1.6049 Evaluate side-chains 11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2151 Z= 0.217 Angle : 0.471 5.268 2957 Z= 0.267 Chirality : 0.039 0.115 368 Planarity : 0.003 0.028 354 Dihedral : 4.365 20.696 308 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.99 % Allowed : 12.32 % Favored : 86.70 % 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 (0.52), residues: 275 helix: 2.24 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.17 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.227 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.0726 time to fit residues: 1.5835 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 0.0020 chunk 23 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 overall best weight: 0.1664 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2151 Z= 0.120 Angle : 0.411 5.142 2957 Z= 0.229 Chirality : 0.037 0.108 368 Planarity : 0.003 0.028 354 Dihedral : 4.046 20.871 308 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.99 % Allowed : 12.81 % Favored : 86.21 % 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: 2.74 (0.52), residues: 275 helix: 2.45 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -1.16 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.007 0.001 PHE R 108 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.226 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 0.0712 time to fit residues: 1.5046 Evaluate side-chains 10 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2151 Z= 0.251 Angle : 0.487 5.254 2957 Z= 0.275 Chirality : 0.040 0.114 368 Planarity : 0.004 0.028 354 Dihedral : 4.335 20.086 308 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.49 (0.52), residues: 275 helix: 2.29 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.20 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.012 0.002 TYR R 199 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.199 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0665 time to fit residues: 1.4692 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.200 Angle : 0.463 5.231 2957 Z= 0.260 Chirality : 0.039 0.116 368 Planarity : 0.003 0.028 354 Dihedral : 4.303 20.626 308 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.46 (0.52), residues: 275 helix: 2.27 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.23 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.283 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0863 time to fit residues: 2.0387 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2151 Z= 0.158 Angle : 0.436 5.218 2957 Z= 0.244 Chirality : 0.038 0.112 368 Planarity : 0.003 0.028 354 Dihedral : 4.155 20.959 308 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.60 (0.52), residues: 275 helix: 2.37 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.21 (0.81), residues: 53 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 0.007 0.001 PHE R 61 TYR 0.008 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.216 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0636 time to fit residues: 1.3762 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.134681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119740 restraints weight = 2820.004| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.79 r_work: 0.3257 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2151 Z= 0.160 Angle : 0.436 5.198 2957 Z= 0.244 Chirality : 0.038 0.111 368 Planarity : 0.003 0.028 354 Dihedral : 4.119 20.743 308 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.64 (0.51), residues: 275 helix: 2.41 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.25 (0.80), residues: 53 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 0.007 0.001 PHE R 61 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 941.59 seconds wall clock time: 21 minutes 59.23 seconds (1319.23 seconds total)