Starting phenix.real_space_refine on Wed Nov 13 23:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggz_40026/11_2024/8ggz_40026.cif" } resolution = 3.9 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= 0.017 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 9 5.16 5 C 1324 2.51 5 N 327 2.21 5 O 334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1994 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1979 Classifications: {'peptide': 281} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 90} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 124 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: 3.43, per 1000 atoms: 1.72 Number of scatterers: 1994 At special positions: 0 Unit cell: (56.4005, 85.0346, 61.6067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 334 8.00 N 327 7.00 C 1324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 330.9 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 536 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.941A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.307A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.938A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.635A 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 164 removed outlier: 3.602A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 181 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 297 removed outlier: 4.013A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.934A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 316 Processing helix chain 'R' and resid 317 through 320 Processing helix chain 'R' and resid 321 through 326 Processing helix chain 'R' and resid 329 through 338 162 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: 0.52 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 615 1.34 - 1.46: 532 1.46 - 1.58: 889 1.58 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2049 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.542 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 2044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2674 1.12 - 2.24: 111 2.24 - 3.36: 24 3.36 - 4.48: 5 4.48 - 5.60: 6 Bond angle restraints: 2820 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.60e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 123.05 126.25 -3.20 1.57e+00 4.06e-01 4.16e+00 angle pdb=" C TRP R 173 " pdb=" N TYR R 174 " pdb=" CA TYR R 174 " ideal model delta sigma weight residual 123.91 127.07 -3.16 1.66e+00 3.63e-01 3.63e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.10 -5.47 3.00e+00 1.11e-01 3.32e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.29 117.75 2.54 1.42e+00 4.96e-01 3.19e+00 ... (remaining 2815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 1044 15.45 - 30.90: 80 30.90 - 46.35: 23 46.35 - 61.79: 1 61.79 - 77.24: 2 Dihedral angle restraints: 1150 sinusoidal: 324 harmonic: 826 Sorted by residual: 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 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG R 131 " pdb=" CB ARG R 131 " pdb=" CG ARG R 131 " pdb=" CD ARG R 131 " ideal model delta sinusoidal sigma weight residual -180.00 -128.30 -51.70 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA MET R 82 " pdb=" CB MET R 82 " pdb=" CG MET R 82 " pdb=" SD MET R 82 " ideal model delta sinusoidal sigma weight residual 180.00 -134.27 -45.73 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 1147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 235 0.036 - 0.072: 87 0.072 - 0.108: 14 0.108 - 0.143: 1 0.143 - 0.179: 1 Chirality restraints: 338 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.58 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA TYR R 174 " pdb=" N TYR R 174 " pdb=" C TYR R 174 " pdb=" CB TYR R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.04e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.75e-01 ... (remaining 335 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO R 138 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 108 " 0.009 2.00e-02 2.50e+03 8.48e-03 1.26e+00 pdb=" CG PHE R 108 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 108 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 173 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C TRP R 173 " -0.018 2.00e-02 2.50e+03 pdb=" O TRP R 173 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR R 174 " 0.006 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 512 2.80 - 3.33: 2010 3.33 - 3.85: 3195 3.85 - 4.38: 2923 4.38 - 4.90: 5562 Nonbonded interactions: 14202 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.278 3.040 nonbonded pdb=" O LEU R 324 " pdb=" NH1 ARG R 328 " model vdw 2.366 3.120 nonbonded pdb=" OD1 ASP R 192 " pdb=" N PHE R 193 " model vdw 2.386 3.120 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.529 3.120 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.633 2.496 ... (remaining 14197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.950 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2049 Z= 0.221 Angle : 0.580 5.601 2820 Z= 0.326 Chirality : 0.038 0.179 338 Planarity : 0.004 0.055 350 Dihedral : 12.741 77.243 614 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.53), residues: 277 helix: 2.79 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.26 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.019 0.001 PHE R 108 TYR 0.010 0.001 TYR R 219 ARG 0.002 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.197 Fit side-chains REVERT: R 131 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7616 (mtp85) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1200 time to fit residues: 7.3497 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2049 Z= 0.142 Angle : 0.483 4.740 2820 Z= 0.263 Chirality : 0.038 0.118 338 Planarity : 0.004 0.040 350 Dihedral : 3.774 17.893 309 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.37 % Allowed : 14.01 % Favored : 79.62 % 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: 2.51 (0.54), residues: 277 helix: 2.71 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.00 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.015 0.001 PHE R 289 TYR 0.017 0.002 TYR R 308 ARG 0.003 0.001 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.195 Fit side-chains REVERT: R 131 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7424 (ttt90) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.1008 time to fit residues: 5.0128 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 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: 0.7854 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2049 Z= 0.173 Angle : 0.506 5.091 2820 Z= 0.277 Chirality : 0.039 0.121 338 Planarity : 0.004 0.044 350 Dihedral : 3.830 17.674 309 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.10 % Allowed : 19.75 % Favored : 75.16 % 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: 2.60 (0.53), residues: 277 helix: 2.80 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.84 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 108 TYR 0.014 0.002 TYR R 141 ARG 0.002 0.001 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.168 Fit side-chains REVERT: R 131 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7422 (ttt90) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1069 time to fit residues: 4.6165 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.0030 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4708 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2049 Z= 0.146 Angle : 0.477 4.764 2820 Z= 0.262 Chirality : 0.038 0.123 338 Planarity : 0.004 0.043 350 Dihedral : 3.772 17.749 309 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.73 % Allowed : 19.75 % Favored : 74.52 % 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: 2.59 (0.53), residues: 277 helix: 2.81 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.91 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.009 0.001 PHE R 289 TYR 0.012 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.220 Fit side-chains REVERT: R 131 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7418 (ttt90) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.0884 time to fit residues: 3.9960 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2049 Z= 0.171 Angle : 0.491 4.777 2820 Z= 0.273 Chirality : 0.039 0.121 338 Planarity : 0.004 0.044 350 Dihedral : 3.879 17.995 309 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.01 % Allowed : 21.66 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.53), residues: 277 helix: 2.75 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.93 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.009 0.001 PHE R 289 TYR 0.013 0.001 TYR R 141 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.181 Fit side-chains REVERT: R 131 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7392 (ttt90) outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 0.1122 time to fit residues: 5.0195 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.2818 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2049 Z= 0.137 Angle : 0.486 5.992 2820 Z= 0.257 Chirality : 0.038 0.121 338 Planarity : 0.003 0.040 350 Dihedral : 3.702 17.843 309 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.18 % Allowed : 25.48 % Favored : 71.34 % 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: 2.55 (0.54), residues: 277 helix: 2.65 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.95 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 289 TYR 0.012 0.001 TYR R 174 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.204 Fit side-chains REVERT: R 131 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7403 (ttt90) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.1034 time to fit residues: 4.4939 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0570 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2049 Z= 0.166 Angle : 0.495 5.364 2820 Z= 0.269 Chirality : 0.038 0.121 338 Planarity : 0.004 0.047 350 Dihedral : 3.815 17.664 309 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.73 % Allowed : 22.93 % Favored : 71.34 % 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 (0.54), residues: 277 helix: 2.62 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.79 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.008 0.001 PHE R 289 TYR 0.012 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.226 Fit side-chains REVERT: R 131 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7422 (ttt90) outliers start: 9 outliers final: 9 residues processed: 32 average time/residue: 0.1134 time to fit residues: 4.4830 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2049 Z= 0.132 Angle : 0.472 5.091 2820 Z= 0.254 Chirality : 0.038 0.120 338 Planarity : 0.003 0.045 350 Dihedral : 3.704 17.694 309 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.10 % Allowed : 23.57 % Favored : 71.34 % 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 (0.54), residues: 277 helix: 2.61 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.82 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.006 0.001 PHE R 108 TYR 0.011 0.001 TYR R 174 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.218 Fit side-chains REVERT: R 131 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7426 (ttt90) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1075 time to fit residues: 4.7988 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2049 Z= 0.192 Angle : 0.523 4.812 2820 Z= 0.287 Chirality : 0.039 0.124 338 Planarity : 0.004 0.052 350 Dihedral : 3.946 17.815 309 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.73 % Allowed : 22.93 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.54), residues: 277 helix: 2.66 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -1.79 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 290 TYR 0.012 0.002 TYR R 308 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.259 Fit side-chains REVERT: R 131 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7424 (ttt90) outliers start: 9 outliers final: 9 residues processed: 34 average time/residue: 0.1437 time to fit residues: 5.8065 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2049 Z= 0.168 Angle : 0.508 4.743 2820 Z= 0.276 Chirality : 0.039 0.123 338 Planarity : 0.004 0.052 350 Dihedral : 3.909 18.022 309 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.10 % Allowed : 24.84 % Favored : 70.06 % 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: 2.37 (0.54), residues: 277 helix: 2.71 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.06 (0.75), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.006 0.001 PHE R 289 TYR 0.011 0.001 TYR R 308 ARG 0.002 0.000 ARG R 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.229 Fit side-chains REVERT: R 131 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7394 (ttt90) outliers start: 8 outliers final: 8 residues processed: 34 average time/residue: 0.1103 time to fit residues: 4.6308 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 9 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127478 restraints weight = 3777.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130095 restraints weight = 1979.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131889 restraints weight = 1241.050| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2049 Z= 0.194 Angle : 0.528 4.728 2820 Z= 0.291 Chirality : 0.039 0.124 338 Planarity : 0.004 0.050 350 Dihedral : 4.020 18.154 309 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.73 % Allowed : 25.48 % Favored : 68.79 % 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: 2.26 (0.53), residues: 277 helix: 2.60 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -2.07 (0.73), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.009 0.003 HIS R 178 PHE 0.008 0.001 PHE R 289 TYR 0.012 0.002 TYR R 308 ARG 0.002 0.000 ARG R 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 909.53 seconds wall clock time: 20 minutes 33.74 seconds (1233.74 seconds total)