Starting phenix.real_space_refine on Wed Nov 13 23:31:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/11_2024/8ggn_40014.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1446 2.51 5 N 344 2.21 5 O 363 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: 2168 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2153 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 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: 2.36, per 1000 atoms: 1.09 Number of scatterers: 2168 At special positions: 0 Unit cell: (58.1359, 83.2992, 61.6067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 363 8.00 N 344 7.00 C 1446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 250.8 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.753A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.251A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.640A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.696A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.583A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.007A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.619A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.567A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.765A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 168 hydrogen bonds defined for protein. 504 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: 0.51 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 325 1.32 - 1.44: 650 1.44 - 1.56: 1228 1.56 - 1.69: 1 1.69 - 1.81: 21 Bond restraints: 2225 Sorted by residual: bond pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.74e+00 bond pdb=" C LEU R 64 " pdb=" O LEU R 64 " ideal model delta sigma weight residual 1.235 1.199 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.29e+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 5.56e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 2220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2898 1.12 - 2.25: 120 2.25 - 3.37: 17 3.37 - 4.50: 8 4.50 - 5.62: 7 Bond angle restraints: 3050 Sorted by residual: angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" CB GLU R 62 " ideal model delta sigma weight residual 110.49 105.04 5.45 1.48e+00 4.57e-01 1.36e+01 angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" C GLU R 62 " ideal model delta sigma weight residual 113.17 116.58 -3.41 1.26e+00 6.30e-01 7.33e+00 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 113.23 109.94 3.29 1.24e+00 6.50e-01 7.02e+00 angle pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta sigma weight residual 120.82 117.78 3.04 1.55e+00 4.16e-01 3.85e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.96 -5.33 3.00e+00 1.11e-01 3.16e+00 ... (remaining 3045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 1147 16.05 - 32.09: 99 32.09 - 48.14: 20 48.14 - 64.18: 2 64.18 - 80.23: 4 Dihedral angle restraints: 1272 sinusoidal: 432 harmonic: 840 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 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG R 175 " pdb=" CD ARG R 175 " pdb=" NE ARG R 175 " pdb=" CZ ARG R 175 " ideal model delta sinusoidal sigma weight residual -180.00 -139.14 -40.86 2 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CB GLU R 122 " pdb=" CG GLU R 122 " pdb=" CD GLU R 122 " pdb=" OE1 GLU R 122 " ideal model delta sinusoidal sigma weight residual 0.00 80.23 -80.23 1 3.00e+01 1.11e-03 8.86e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 243 0.034 - 0.068: 99 0.068 - 0.101: 23 0.101 - 0.135: 7 0.135 - 0.169: 2 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA LEU R 64 " pdb=" N LEU R 64 " pdb=" C LEU R 64 " pdb=" CB LEU R 64 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 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 2.54 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 371 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 61 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C PHE R 61 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE R 61 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU R 62 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.009 2.00e-02 2.50e+03 6.35e-03 1.01e+00 pdb=" CG TRP R 173 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 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 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.017 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO R 211 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.014 5.00e-02 4.00e+02 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 472 2.78 - 3.31: 2101 3.31 - 3.84: 3495 3.84 - 4.37: 3607 4.37 - 4.90: 6804 Nonbonded interactions: 16479 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.248 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.294 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.438 3.040 nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.448 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.462 3.040 ... (remaining 16474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.440 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2225 Z= 0.319 Angle : 0.584 5.623 3050 Z= 0.331 Chirality : 0.040 0.169 374 Planarity : 0.003 0.025 366 Dihedral : 13.181 80.230 723 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 2.26 (0.49), residues: 281 helix: 2.30 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.013 0.001 PHE R 108 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1778 time to fit residues: 4.8925 Evaluate side-chains 18 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2225 Z= 0.203 Angle : 0.486 5.507 3050 Z= 0.274 Chirality : 0.038 0.126 374 Planarity : 0.003 0.026 366 Dihedral : 4.934 20.523 316 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.40 % Allowed : 6.54 % Favored : 92.06 % 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: 2.76 (0.49), residues: 281 helix: 2.64 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.69 (0.67), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 108 TYR 0.009 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.226 Fit side-chains REVERT: R 63 ARG cc_start: 0.8167 (ptp90) cc_final: 0.6329 (mmt90) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.1762 time to fit residues: 5.6375 Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2225 Z= 0.193 Angle : 0.456 5.317 3050 Z= 0.255 Chirality : 0.037 0.122 374 Planarity : 0.003 0.026 366 Dihedral : 4.569 20.506 316 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 8.41 % Favored : 88.79 % 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: 2.93 (0.49), residues: 281 helix: 2.76 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.77 (0.67), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 217 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.198 Fit side-chains REVERT: R 63 ARG cc_start: 0.7980 (ptp90) cc_final: 0.6266 (mmt90) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1424 time to fit residues: 4.5910 Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2225 Z= 0.256 Angle : 0.488 5.402 3050 Z= 0.274 Chirality : 0.038 0.124 374 Planarity : 0.003 0.028 366 Dihedral : 4.718 20.578 316 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 11.21 % Favored : 86.45 % 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: 2.85 (0.49), residues: 281 helix: 2.71 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.76 (0.68), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.237 Fit side-chains REVERT: R 63 ARG cc_start: 0.7963 (ptp90) cc_final: 0.6241 (mmt90) REVERT: R 101 PHE cc_start: 0.8368 (m-80) cc_final: 0.8022 (m-80) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.2316 time to fit residues: 7.1645 Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE 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: 1.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.0040 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2225 Z= 0.174 Angle : 0.438 5.297 3050 Z= 0.245 Chirality : 0.037 0.120 374 Planarity : 0.003 0.027 366 Dihedral : 4.424 20.532 316 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 11.21 % Favored : 86.45 % 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: 3.07 (0.50), residues: 281 helix: 2.88 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.78 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 217 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.179 Fit side-chains REVERT: R 63 ARG cc_start: 0.7930 (ptp90) cc_final: 0.6154 (mmt90) REVERT: R 101 PHE cc_start: 0.8322 (m-80) cc_final: 0.7998 (m-80) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1312 time to fit residues: 4.0310 Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2225 Z= 0.118 Angle : 0.401 5.214 3050 Z= 0.221 Chirality : 0.036 0.115 374 Planarity : 0.003 0.025 366 Dihedral : 4.087 20.111 316 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.27 % Allowed : 11.68 % Favored : 85.05 % 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: 3.43 (0.50), residues: 281 helix: 3.09 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.59 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.001 0.000 HIS R 296 PHE 0.007 0.001 PHE R 108 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.235 Fit side-chains REVERT: R 63 ARG cc_start: 0.7903 (ptp90) cc_final: 0.6193 (mmt90) outliers start: 7 outliers final: 3 residues processed: 27 average time/residue: 0.1426 time to fit residues: 4.7315 Evaluate side-chains 24 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2225 Z= 0.184 Angle : 0.444 5.317 3050 Z= 0.248 Chirality : 0.037 0.119 374 Planarity : 0.003 0.025 366 Dihedral : 4.207 20.045 316 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 12.62 % Favored : 84.58 % 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: 3.26 (0.50), residues: 281 helix: 2.91 (0.34), residues: 227 sheet: None (None), residues: 0 loop : -1.42 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 101 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.228 Fit side-chains REVERT: R 63 ARG cc_start: 0.7884 (ptp90) cc_final: 0.6140 (mmt90) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1799 time to fit residues: 5.7814 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2225 Z= 0.209 Angle : 0.458 5.320 3050 Z= 0.257 Chirality : 0.038 0.120 374 Planarity : 0.003 0.026 366 Dihedral : 4.338 20.215 316 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 12.15 % Favored : 85.05 % 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: 3.11 (0.50), residues: 281 helix: 2.87 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.59 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.213 Fit side-chains REVERT: R 63 ARG cc_start: 0.7925 (ptp90) cc_final: 0.6128 (mmt90) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1873 time to fit residues: 6.0776 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2225 Z= 0.184 Angle : 0.444 5.311 3050 Z= 0.248 Chirality : 0.037 0.119 374 Planarity : 0.003 0.026 366 Dihedral : 4.265 20.397 316 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 12.62 % Favored : 84.58 % 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: 3.15 (0.50), residues: 281 helix: 2.94 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.71 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 101 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.234 Fit side-chains REVERT: R 63 ARG cc_start: 0.7907 (ptp90) cc_final: 0.6123 (mmt90) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1726 time to fit residues: 5.5451 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE 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: 0.5980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2225 Z= 0.197 Angle : 0.451 5.316 3050 Z= 0.253 Chirality : 0.037 0.119 374 Planarity : 0.003 0.026 366 Dihedral : 4.298 20.318 316 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 12.62 % Favored : 84.58 % 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: 3.11 (0.50), residues: 281 helix: 2.91 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.72 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7899 (ptp90) cc_final: 0.6123 (mmt90) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.1624 time to fit residues: 5.4602 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.125430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108259 restraints weight = 2753.330| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.57 r_work: 0.3067 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2225 Z= 0.205 Angle : 0.456 5.323 3050 Z= 0.256 Chirality : 0.038 0.120 374 Planarity : 0.003 0.026 366 Dihedral : 4.339 20.380 316 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.27 % Allowed : 12.15 % Favored : 84.58 % 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: 3.08 (0.50), residues: 281 helix: 2.88 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.71 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.65 seconds wall clock time: 17 minutes 45.44 seconds (1065.44 seconds total)