Starting phenix.real_space_refine on Wed Nov 13 23:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggw_40023/11_2024/8ggw_40023.cif" } resolution = 3.6 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= 0.020 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 12 5.16 5 C 1379 2.51 5 N 335 2.21 5 O 353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2079 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2064 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 1.26 Number of scatterers: 2079 At special positions: 0 Unit cell: (54.6651, 83.2992, 62.4744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 353 8.00 N 335 7.00 C 1379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 232.3 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.627A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.643A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.847A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.790A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.619A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.883A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 Proline residue: R 288 - end of helix removed outlier: 3.918A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.874A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 161 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 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: 638 1.34 - 1.46: 583 1.46 - 1.58: 897 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2135 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.25e+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 4.85e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.323 0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 2130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 2771 1.18 - 2.35: 128 2.35 - 3.53: 22 3.53 - 4.71: 7 4.71 - 5.88: 6 Bond angle restraints: 2934 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 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 121.58 116.00 5.58 1.95e+00 2.63e-01 8.20e+00 angle pdb=" N ILE R 135 " pdb=" CA ILE R 135 " pdb=" C ILE R 135 " ideal model delta sigma weight residual 111.00 113.67 -2.67 1.09e+00 8.42e-01 6.01e+00 angle pdb=" C ILE R 135 " pdb=" CA ILE R 135 " pdb=" CB ILE R 135 " ideal model delta sigma weight residual 112.24 109.57 2.67 1.34e+00 5.57e-01 3.98e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.41 113.75 -3.34 1.68e+00 3.54e-01 3.96e+00 ... (remaining 2929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1094 16.95 - 33.91: 103 33.91 - 50.86: 15 50.86 - 67.82: 0 67.82 - 84.77: 1 Dihedral angle restraints: 1213 sinusoidal: 385 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 177.77 -84.77 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CA CYS R 190 " pdb=" C CYS R 190 " pdb=" N CYS R 191 " pdb=" CA CYS R 191 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 227 0.033 - 0.066: 90 0.066 - 0.098: 31 0.098 - 0.131: 5 0.131 - 0.164: 1 Chirality restraints: 354 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE R 303 " pdb=" N ILE R 303 " pdb=" C ILE R 303 " pdb=" CB ILE R 303 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA TYR R 219 " pdb=" N TYR R 219 " pdb=" C TYR R 219 " pdb=" CB TYR R 219 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 351 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 330 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.011 2.00e-02 2.50e+03 8.68e-03 1.88e+00 pdb=" CG TRP R 173 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO R 168 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.015 5.00e-02 4.00e+02 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 424 2.77 - 3.30: 2103 3.30 - 3.84: 3391 3.84 - 4.37: 3303 4.37 - 4.90: 6123 Nonbonded interactions: 15344 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.241 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR R 118 " pdb=" OG SER R 161 " model vdw 2.338 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.449 3.120 nonbonded pdb=" O VAL R 292 " pdb=" ND1 HIS R 296 " model vdw 2.581 3.120 ... (remaining 15339 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 0.054 2135 Z= 0.231 Angle : 0.621 5.882 2934 Z= 0.353 Chirality : 0.040 0.164 354 Planarity : 0.004 0.037 361 Dihedral : 12.729 44.728 669 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 2.12 (0.50), residues: 277 helix: 2.43 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -1.87 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 173 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 290 TYR 0.014 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.221 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1376 time to fit residues: 6.5337 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.158 Angle : 0.524 4.992 2934 Z= 0.291 Chirality : 0.040 0.137 354 Planarity : 0.004 0.032 361 Dihedral : 5.051 18.695 311 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.66 % Allowed : 12.77 % Favored : 84.57 % 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: 2.25 (0.51), residues: 277 helix: 2.39 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.89 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 173 HIS 0.001 0.000 HIS R 178 PHE 0.006 0.001 PHE R 217 TYR 0.014 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.318 Fit side-chains REVERT: R 163 LEU cc_start: 0.8047 (mm) cc_final: 0.7739 (tt) REVERT: R 173 TRP cc_start: 0.7129 (m-10) cc_final: 0.6594 (m-90) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.1341 time to fit residues: 5.8903 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7672 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2135 Z= 0.219 Angle : 0.546 5.175 2934 Z= 0.302 Chirality : 0.041 0.130 354 Planarity : 0.004 0.031 361 Dihedral : 4.861 18.496 311 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.19 % Allowed : 15.43 % Favored : 81.38 % 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: 2.24 (0.51), residues: 277 helix: 2.27 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.56 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.011 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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: 6 poor density : 33 time to evaluate : 0.226 Fit side-chains REVERT: R 171 MET cc_start: 0.6892 (ppp) cc_final: 0.6422 (ptm) REVERT: R 173 TRP cc_start: 0.7408 (m-10) cc_final: 0.7035 (m-90) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.1221 time to fit residues: 5.3927 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 : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.0270 chunk 13 optimal weight: 0.0170 chunk 24 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 overall best weight: 0.2874 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2135 Z= 0.145 Angle : 0.490 5.715 2934 Z= 0.268 Chirality : 0.040 0.132 354 Planarity : 0.003 0.029 361 Dihedral : 4.508 17.687 311 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.19 % Allowed : 17.55 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.51), residues: 277 helix: 2.52 (0.35), residues: 218 sheet: None (None), residues: 0 loop : -1.37 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.002 0.000 HIS R 296 PHE 0.008 0.001 PHE R 101 TYR 0.011 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.257 Fit side-chains REVERT: R 40 MET cc_start: 0.8214 (mmm) cc_final: 0.7980 (mmm) REVERT: R 163 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7472 (tt) REVERT: R 171 MET cc_start: 0.6826 (ppp) cc_final: 0.6432 (ptm) REVERT: R 173 TRP cc_start: 0.7327 (m-10) cc_final: 0.7121 (m-10) REVERT: R 178 HIS cc_start: 0.8129 (p90) cc_final: 0.7899 (p90) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.1343 time to fit residues: 5.7189 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 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: 0.7655 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.189 Angle : 0.515 5.764 2934 Z= 0.283 Chirality : 0.040 0.128 354 Planarity : 0.003 0.028 361 Dihedral : 4.539 17.918 311 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.19 % Allowed : 18.62 % Favored : 78.19 % 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: 2.38 (0.51), residues: 277 helix: 2.29 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.64 (0.82), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 61 TYR 0.007 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.227 Fit side-chains REVERT: R 163 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7388 (tt) REVERT: R 171 MET cc_start: 0.6932 (ppp) cc_final: 0.6724 (ptm) REVERT: R 178 HIS cc_start: 0.8167 (p90) cc_final: 0.7903 (p90) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.1323 time to fit residues: 5.6157 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.0000 chunk 17 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.172 Angle : 0.513 6.302 2934 Z= 0.279 Chirality : 0.040 0.126 354 Planarity : 0.003 0.030 361 Dihedral : 4.586 17.866 311 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.26 % Allowed : 17.55 % Favored : 78.19 % 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: 2.59 (0.51), residues: 277 helix: 2.67 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.74 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 101 TYR 0.009 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** 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 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.223 Fit side-chains REVERT: R 163 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7365 (tt) REVERT: R 171 MET cc_start: 0.6977 (ppp) cc_final: 0.5916 (ppp) REVERT: R 173 TRP cc_start: 0.7905 (m-10) cc_final: 0.6747 (m-90) REVERT: R 178 HIS cc_start: 0.8147 (p90) cc_final: 0.7863 (p90) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1384 time to fit residues: 6.0620 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7672 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.195 Angle : 0.529 5.439 2934 Z= 0.291 Chirality : 0.041 0.126 354 Planarity : 0.003 0.030 361 Dihedral : 4.636 18.205 311 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.72 % Allowed : 18.62 % Favored : 77.66 % 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: 2.48 (0.50), residues: 277 helix: 2.60 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.81 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.009 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.229 Fit side-chains REVERT: R 163 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7370 (tt) REVERT: R 173 TRP cc_start: 0.7956 (m-10) cc_final: 0.7155 (m-90) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.1365 time to fit residues: 5.6083 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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: 0.7654 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.179 Angle : 0.522 7.182 2934 Z= 0.284 Chirality : 0.040 0.127 354 Planarity : 0.003 0.028 361 Dihedral : 4.604 18.140 311 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.26 % Allowed : 18.62 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.51), residues: 277 helix: 2.62 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.84 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.008 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 : 0.236 Fit side-chains REVERT: R 115 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7350 (tp) REVERT: R 163 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7380 (tt) REVERT: R 171 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6046 (ppp) REVERT: R 173 TRP cc_start: 0.7843 (m-10) cc_final: 0.6776 (m-90) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.1319 time to fit residues: 5.5970 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.193 Angle : 0.532 6.583 2934 Z= 0.292 Chirality : 0.040 0.126 354 Planarity : 0.003 0.028 361 Dihedral : 4.629 18.232 311 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.26 % Allowed : 19.68 % Favored : 76.06 % 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: 2.42 (0.50), residues: 277 helix: 2.56 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.84 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 290 TYR 0.008 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.265 Fit side-chains REVERT: R 115 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7358 (tp) REVERT: R 171 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6058 (ppp) REVERT: R 173 TRP cc_start: 0.7891 (m-10) cc_final: 0.6892 (m-90) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.1372 time to fit residues: 5.8609 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2135 Z= 0.220 Angle : 0.555 6.590 2934 Z= 0.307 Chirality : 0.041 0.129 354 Planarity : 0.004 0.029 361 Dihedral : 4.733 19.232 311 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.26 % Allowed : 20.21 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.51), residues: 277 helix: 2.44 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.81 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 290 TYR 0.009 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 ********************** 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 : 0.237 Fit side-chains REVERT: R 115 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7369 (tp) REVERT: R 171 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6088 (ppp) REVERT: R 173 TRP cc_start: 0.7947 (m-10) cc_final: 0.6937 (m-10) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.1434 time to fit residues: 5.7253 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.153996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137703 restraints weight = 3271.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141068 restraints weight = 1742.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142677 restraints weight = 1056.507| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.031 2135 Z= 0.173 Angle : 0.520 6.443 2934 Z= 0.285 Chirality : 0.040 0.127 354 Planarity : 0.003 0.027 361 Dihedral : 4.608 18.344 311 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.19 % Allowed : 21.81 % Favored : 75.00 % 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: 2.52 (0.51), residues: 277 helix: 2.55 (0.34), residues: 213 sheet: None (None), residues: 0 loop : -1.56 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.006 0.001 TYR R 141 ARG 0.002 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.66 seconds wall clock time: 22 minutes 4.90 seconds (1324.90 seconds total)