Starting phenix.real_space_refine on Sun Mar 10 14:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y13_33555/03_2024/7y13_33555_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.070 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 22 5.16 5 C 1479 2.51 5 N 342 2.21 5 O 356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2199 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2199 Unusual residues: {'PLM': 7} Classifications: {'peptide': 264, 'undetermined': 7, 'water': 2} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 253, None: 9} Not linked: pdbres="HIS R 285 " pdbres="PLM R 401 " Not linked: pdbres="PLM R 401 " pdbres="PLM R 402 " Not linked: pdbres="PLM R 402 " pdbres="PLM R 403 " Not linked: pdbres="PLM R 403 " pdbres="PLM R 404 " Not linked: pdbres="PLM R 404 " pdbres="PLM R 405 " ... (remaining 4 not shown) Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 1.83, per 1000 atoms: 0.83 Number of scatterers: 2199 At special positions: 0 Unit cell: (56.7, 66.825, 68.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 356 8.00 N 342 7.00 C 1479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'R' and resid 23 through 52 removed outlier: 3.575A pdb=" N LEU R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 Processing helix chain 'R' and resid 97 through 128 removed outlier: 3.632A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 141 through 164 Processing helix chain 'R' and resid 173 through 208 removed outlier: 3.731A pdb=" N ARG R 177 " --> pdb=" O ASP R 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 217 through 244 removed outlier: 4.240A pdb=" N LEU R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) Proline residue: R 236 - end of helix removed outlier: 3.800A pdb=" N TRP R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 276 Proline residue: R 273 - end of helix 154 hydrogen bonds defined for protein. 462 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: 0.52 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 629 1.35 - 1.46: 570 1.46 - 1.58: 1014 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 2246 Sorted by residual: bond pdb=" C2 PLM R 407 " pdb=" C3 PLM R 407 " ideal model delta sigma weight residual 1.522 1.493 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C2 PLM R 405 " pdb=" C3 PLM R 405 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C2 PLM R 403 " pdb=" C3 PLM R 403 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C2 PLM R 406 " pdb=" C3 PLM R 406 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C2 PLM R 401 " pdb=" C3 PLM R 401 " ideal model delta sigma weight residual 1.522 1.497 0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 2241 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.15: 49 106.15 - 113.10: 1208 113.10 - 120.05: 861 120.05 - 127.00: 869 127.00 - 133.96: 32 Bond angle restraints: 3019 Sorted by residual: angle pdb=" CA LEU R 52 " pdb=" CB LEU R 52 " pdb=" CG LEU R 52 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 angle pdb=" C LYS R 166 " pdb=" N PHE R 167 " pdb=" CA PHE R 167 " ideal model delta sigma weight residual 120.17 123.62 -3.45 1.54e+00 4.22e-01 5.01e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.38 3.76 1.75e+00 3.27e-01 4.62e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 117.63 -4.03 1.90e+00 2.77e-01 4.49e+00 angle pdb=" N PHE R 167 " pdb=" CA PHE R 167 " pdb=" C PHE R 167 " ideal model delta sigma weight residual 113.50 110.22 3.28 1.65e+00 3.67e-01 3.94e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1117 11.54 - 23.08: 142 23.08 - 34.63: 59 34.63 - 46.17: 23 46.17 - 57.71: 4 Dihedral angle restraints: 1345 sinusoidal: 563 harmonic: 782 Sorted by residual: dihedral pdb=" CG ARG R 103 " pdb=" CD ARG R 103 " pdb=" NE ARG R 103 " pdb=" CZ ARG R 103 " ideal model delta sinusoidal sigma weight residual -90.00 -134.56 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA HIS R 57 " pdb=" C HIS R 57 " pdb=" N ARG R 58 " pdb=" CA ARG R 58 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB MET R 35 " pdb=" CG MET R 35 " pdb=" SD MET R 35 " pdb=" CE MET R 35 " ideal model delta sinusoidal sigma weight residual 60.00 117.71 -57.71 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 219 0.031 - 0.062: 103 0.062 - 0.092: 20 0.092 - 0.123: 8 0.123 - 0.154: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO R 236 " pdb=" N PRO R 236 " pdb=" C PRO R 236 " pdb=" CB PRO R 236 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 348 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 235 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO R 236 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP R 144 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 187 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C MET R 187 " 0.030 2.00e-02 2.50e+03 pdb=" O MET R 187 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 188 " -0.010 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 134 2.74 - 3.28: 2121 3.28 - 3.82: 3745 3.82 - 4.36: 4147 4.36 - 4.90: 7545 Nonbonded interactions: 17692 Sorted by model distance: nonbonded pdb=" NH2 ARG R 137 " pdb=" OG SER R 142 " model vdw 2.195 2.520 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.211 2.440 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.411 2.520 nonbonded pdb=" OG1 THR R 22 " pdb=" N VAL R 23 " model vdw 2.435 2.520 nonbonded pdb=" O SER R 78 " pdb=" OG SER R 81 " model vdw 2.436 2.440 ... (remaining 17687 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 6.740 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.500 Find NCS groups from input model: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 0.029 2246 Z= 0.328 Angle : 0.676 8.296 3019 Z= 0.339 Chirality : 0.038 0.154 351 Planarity : 0.005 0.075 350 Dihedral : 13.192 57.709 830 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 (0.56), residues: 262 helix: 1.91 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.24 (0.94), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 144 HIS 0.001 0.000 HIS R 57 PHE 0.014 0.001 PHE R 202 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.254 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1192 time to fit residues: 4.9017 Evaluate side-chains 30 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2246 Z= 0.204 Angle : 0.553 7.260 3019 Z= 0.274 Chirality : 0.036 0.144 351 Planarity : 0.005 0.074 350 Dihedral : 8.029 46.528 382 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.86 % Allowed : 6.90 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.56), residues: 262 helix: 2.08 (0.38), residues: 204 sheet: None (None), residues: 0 loop : -1.37 (0.95), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.015 0.001 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.225 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1148 time to fit residues: 4.6770 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2246 Z= 0.157 Angle : 0.515 6.507 3019 Z= 0.259 Chirality : 0.035 0.132 351 Planarity : 0.005 0.072 350 Dihedral : 7.801 46.202 382 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.29 % Allowed : 9.05 % Favored : 89.66 % 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 (0.57), residues: 262 helix: 2.31 (0.38), residues: 204 sheet: None (None), residues: 0 loop : -1.32 (0.96), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.001 0.000 HIS R 57 PHE 0.012 0.001 PHE R 202 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.242 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.1156 time to fit residues: 4.5636 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7675 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2246 Z= 0.229 Angle : 0.574 10.550 3019 Z= 0.283 Chirality : 0.037 0.153 351 Planarity : 0.005 0.073 350 Dihedral : 9.424 57.140 382 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.29 % Allowed : 11.21 % Favored : 87.50 % 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: 2.29 (0.56), residues: 262 helix: 2.16 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.00 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.015 0.001 PHE R 202 TYR 0.007 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.238 Fit side-chains REVERT: R 95 ASP cc_start: 0.7297 (t0) cc_final: 0.6977 (t0) REVERT: R 185 LEU cc_start: 0.8078 (tt) cc_final: 0.7684 (tp) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1177 time to fit residues: 4.9118 Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2246 Z= 0.195 Angle : 0.547 10.427 3019 Z= 0.270 Chirality : 0.036 0.141 351 Planarity : 0.005 0.073 350 Dihedral : 9.301 56.505 382 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 13.36 % Favored : 84.91 % 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: 2.39 (0.57), residues: 262 helix: 2.35 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.26 (0.97), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.014 0.001 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.221 Fit side-chains REVERT: R 185 LEU cc_start: 0.8069 (tt) cc_final: 0.7678 (tp) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.1156 time to fit residues: 4.5324 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2246 Z= 0.194 Angle : 0.546 10.253 3019 Z= 0.270 Chirality : 0.036 0.141 351 Planarity : 0.005 0.073 350 Dihedral : 9.597 58.679 382 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.29 % Allowed : 13.79 % Favored : 84.91 % 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: 2.58 (0.56), residues: 262 helix: 2.36 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.92 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.014 0.001 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.242 Fit side-chains REVERT: R 95 ASP cc_start: 0.7201 (t0) cc_final: 0.6830 (t0) REVERT: R 185 LEU cc_start: 0.8094 (tt) cc_final: 0.7697 (tp) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.1205 time to fit residues: 4.8477 Evaluate side-chains 35 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2246 Z= 0.176 Angle : 0.535 10.355 3019 Z= 0.264 Chirality : 0.036 0.137 351 Planarity : 0.005 0.072 350 Dihedral : 9.637 59.922 382 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.29 % Allowed : 15.09 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.56), residues: 262 helix: 2.48 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.85 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 144 HIS 0.001 0.000 HIS R 57 PHE 0.018 0.001 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.263 Fit side-chains REVERT: R 185 LEU cc_start: 0.8115 (tt) cc_final: 0.7711 (tp) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.1315 time to fit residues: 5.2569 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2246 Z= 0.144 Angle : 0.515 10.128 3019 Z= 0.255 Chirality : 0.035 0.126 351 Planarity : 0.005 0.071 350 Dihedral : 9.297 57.188 382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.72 % Allowed : 14.66 % Favored : 83.62 % 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: 2.82 (0.57), residues: 262 helix: 2.68 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.23 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 144 HIS 0.001 0.000 HIS R 57 PHE 0.021 0.001 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.239 Fit side-chains REVERT: R 185 LEU cc_start: 0.8145 (tt) cc_final: 0.7709 (tp) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.1195 time to fit residues: 4.8462 Evaluate side-chains 32 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2246 Z= 0.210 Angle : 0.554 10.285 3019 Z= 0.274 Chirality : 0.037 0.147 351 Planarity : 0.005 0.072 350 Dihedral : 9.726 58.324 382 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.72 % Allowed : 15.09 % Favored : 83.19 % 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: 2.76 (0.56), residues: 262 helix: 2.47 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.75 (1.03), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.020 0.002 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.247 Fit side-chains REVERT: R 185 LEU cc_start: 0.8130 (tt) cc_final: 0.7709 (tp) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.1340 time to fit residues: 5.1938 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2246 Z= 0.241 Angle : 0.583 10.384 3019 Z= 0.289 Chirality : 0.038 0.151 351 Planarity : 0.005 0.073 350 Dihedral : 10.083 58.675 382 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.29 % Allowed : 15.52 % Favored : 83.19 % 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 (0.56), residues: 262 helix: 2.34 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.74 (1.04), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.021 0.002 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.240 Fit side-chains REVERT: R 185 LEU cc_start: 0.8097 (tt) cc_final: 0.7720 (tp) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.1184 time to fit residues: 4.6467 Evaluate side-chains 31 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.181787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139770 restraints weight = 2156.728| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.85 r_work: 0.3230 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2246 Z= 0.198 Angle : 0.554 10.290 3019 Z= 0.276 Chirality : 0.036 0.140 351 Planarity : 0.005 0.072 350 Dihedral : 9.857 58.590 382 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.29 % Allowed : 15.52 % Favored : 83.19 % 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: 2.69 (0.56), residues: 262 helix: 2.42 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.78 (1.02), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.024 0.002 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.15 seconds wall clock time: 18 minutes 40.72 seconds (1120.72 seconds total)