Starting phenix.real_space_refine on Thu Dec 7 17:44:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2023/6m7d_30129.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 14 5.16 5 C 2054 2.51 5 N 552 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 2.36, per 1000 atoms: 0.72 Number of scatterers: 3280 At special positions: 0 Unit cell: (78.52, 81.64, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 6 15.00 O 654 8.00 N 552 7.00 C 2054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 611.0 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.5% alpha, 5.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.144A pdb=" N LYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.224A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.763A pdb=" N VAL A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 307 through 313 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 387 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.533A pdb=" N SER A 33 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 102 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 35 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 37 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 106 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LYS A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 105 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O TYR A 127 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 683 1.33 - 1.45: 765 1.45 - 1.57: 1863 1.57 - 1.69: 11 1.69 - 1.81: 26 Bond restraints: 3348 Sorted by residual: bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.85e+00 bond pdb=" N MET A 125 " pdb=" CA MET A 125 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.22e-02 6.72e+03 8.47e+00 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 105 106.45 - 113.33: 1851 113.33 - 120.22: 1305 120.22 - 127.10: 1271 127.10 - 133.98: 24 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CA ASP A 405 " pdb=" C ASP A 405 " pdb=" O ASP A 405 " ideal model delta sigma weight residual 122.63 118.22 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" N THR A 272 " pdb=" CA THR A 272 " pdb=" C THR A 272 " ideal model delta sigma weight residual 111.28 107.63 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C ASN A 241 " pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 120.28 124.74 -4.46 1.34e+00 5.57e-01 1.11e+01 angle pdb=" C SER A 402 " pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 120.00 123.63 -3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" O ARG A 149 " ideal model delta sigma weight residual 121.56 118.10 3.46 1.09e+00 8.42e-01 1.01e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1807 17.82 - 35.64: 155 35.64 - 53.46: 30 53.46 - 71.28: 6 71.28 - 89.10: 3 Dihedral angle restraints: 2001 sinusoidal: 823 harmonic: 1178 Sorted by residual: dihedral pdb=" C GLU A 278 " pdb=" N GLU A 278 " pdb=" CA GLU A 278 " pdb=" CB GLU A 278 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual -90.00 -159.31 69.31 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " pdb=" CD GLU A 214 " pdb=" OE1 GLU A 214 " ideal model delta sinusoidal sigma weight residual 0.00 89.10 -89.10 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 286 0.046 - 0.092: 152 0.092 - 0.139: 69 0.139 - 0.185: 17 0.185 - 0.231: 9 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 530 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.031 2.00e-02 2.50e+03 1.53e-02 5.25e+00 pdb=" N1 U B 2 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 240 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C MET A 240 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 241 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 44 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C VAL A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 115 2.71 - 3.25: 3405 3.25 - 3.80: 5504 3.80 - 4.35: 7360 4.35 - 4.90: 11397 Nonbonded interactions: 27781 Sorted by model distance: nonbonded pdb=" O ALA A 346 " pdb=" O2' U B 4 " model vdw 2.157 2.440 nonbonded pdb=" O THR A 183 " pdb=" O2' U B 2 " model vdw 2.198 2.440 nonbonded pdb=" O ALA A 325 " pdb=" ND2 ASN A 328 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN A 173 " pdb=" O LEU A 209 " model vdw 2.220 2.520 nonbonded pdb=" OD2 ASP A 202 " pdb=" OG1 THR A 204 " model vdw 2.262 2.440 ... (remaining 27776 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 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: 7.380 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: 27.760 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.056 3348 Z= 0.657 Angle : 1.033 5.361 4556 Z= 0.761 Chirality : 0.069 0.231 533 Planarity : 0.005 0.041 564 Dihedral : 13.842 89.104 1249 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.58 % Allowed : 13.12 % Favored : 86.30 % 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: -0.46 (0.38), residues: 410 helix: -0.14 (0.32), residues: 244 sheet: -0.49 (1.15), residues: 23 loop : -0.28 (0.41), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.004 0.001 HIS A 397 PHE 0.016 0.002 PHE A 193 TYR 0.011 0.002 TYR A 275 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.352 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 1.4293 time to fit residues: 99.6761 Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 93 ASN A 140 ASN A 227 GLN A 241 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 288 ASN A 366 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.173 Angle : 0.473 4.767 4556 Z= 0.257 Chirality : 0.040 0.151 533 Planarity : 0.004 0.032 564 Dihedral : 4.822 24.587 515 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.92 % Allowed : 14.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.39), residues: 410 helix: 0.92 (0.33), residues: 241 sheet: -0.03 (1.02), residues: 23 loop : 0.58 (0.45), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 PHE 0.011 0.002 PHE A 269 TYR 0.008 0.001 TYR A 275 ARG 0.005 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.321 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 1.2497 time to fit residues: 72.0466 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1779 time to fit residues: 0.9374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3348 Z= 0.178 Angle : 0.451 4.864 4556 Z= 0.242 Chirality : 0.040 0.132 533 Planarity : 0.003 0.031 564 Dihedral : 4.747 27.336 515 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.92 % Allowed : 15.45 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.40), residues: 410 helix: 1.25 (0.34), residues: 243 sheet: 0.10 (0.94), residues: 25 loop : 1.01 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 PHE 0.011 0.002 PHE A 269 TYR 0.007 0.001 TYR A 275 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.371 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 1.2353 time to fit residues: 64.9791 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3348 Z= 0.137 Angle : 0.425 4.797 4556 Z= 0.228 Chirality : 0.038 0.123 533 Planarity : 0.003 0.030 564 Dihedral : 4.679 29.422 515 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.79 % Allowed : 15.45 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.41), residues: 410 helix: 1.56 (0.34), residues: 243 sheet: 0.43 (0.94), residues: 25 loop : 1.11 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 333 HIS 0.001 0.001 HIS A 396 PHE 0.012 0.001 PHE A 269 TYR 0.007 0.001 TYR A 275 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.336 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 51 average time/residue: 1.2177 time to fit residues: 64.0737 Evaluate side-chains 48 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1610 time to fit residues: 0.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN A 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.176 Angle : 0.459 7.841 4556 Z= 0.237 Chirality : 0.039 0.117 533 Planarity : 0.003 0.030 564 Dihedral : 4.705 28.025 515 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.92 % Allowed : 16.91 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.41), residues: 410 helix: 1.58 (0.34), residues: 242 sheet: 0.58 (0.94), residues: 25 loop : 1.21 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.012 0.001 PHE A 269 TYR 0.007 0.001 TYR A 303 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.355 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 1.1620 time to fit residues: 56.4337 Evaluate side-chains 46 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3348 Z= 0.242 Angle : 0.492 7.498 4556 Z= 0.255 Chirality : 0.041 0.129 533 Planarity : 0.003 0.030 564 Dihedral : 4.851 29.873 515 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.50 % Allowed : 16.03 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.41), residues: 410 helix: 1.44 (0.34), residues: 241 sheet: 0.82 (0.95), residues: 25 loop : 1.24 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 PHE 0.011 0.002 PHE A 193 TYR 0.008 0.001 TYR A 303 ARG 0.005 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.387 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 1.3492 time to fit residues: 70.8258 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.181 Angle : 0.464 6.744 4556 Z= 0.241 Chirality : 0.040 0.129 533 Planarity : 0.003 0.030 564 Dihedral : 4.741 26.213 515 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.08 % Allowed : 16.03 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.41), residues: 410 helix: 1.51 (0.34), residues: 241 sheet: 0.92 (0.95), residues: 25 loop : 1.21 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 PHE 0.011 0.001 PHE A 269 TYR 0.007 0.001 TYR A 303 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.407 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 1.0760 time to fit residues: 56.8233 Evaluate side-chains 44 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3348 Z= 0.152 Angle : 0.455 6.773 4556 Z= 0.235 Chirality : 0.039 0.130 533 Planarity : 0.003 0.029 564 Dihedral : 4.693 28.296 515 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.62 % Allowed : 17.49 % Favored : 79.88 % 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: 2.07 (0.41), residues: 410 helix: 1.61 (0.34), residues: 243 sheet: 0.97 (0.96), residues: 25 loop : 1.28 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.011 0.001 PHE A 269 TYR 0.007 0.001 TYR A 275 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.379 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 1.0456 time to fit residues: 56.3631 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.185 Angle : 0.474 6.707 4556 Z= 0.245 Chirality : 0.040 0.164 533 Planarity : 0.003 0.029 564 Dihedral : 4.721 27.436 515 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.62 % Allowed : 18.66 % Favored : 78.72 % 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: 2.00 (0.41), residues: 410 helix: 1.56 (0.34), residues: 242 sheet: 0.83 (0.94), residues: 25 loop : 1.27 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.010 0.001 PHE A 269 TYR 0.008 0.001 TYR A 127 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.374 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 1.1228 time to fit residues: 53.5574 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.174 Angle : 0.479 6.869 4556 Z= 0.247 Chirality : 0.040 0.189 533 Planarity : 0.003 0.029 564 Dihedral : 4.699 27.225 515 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.04 % Allowed : 18.95 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.41), residues: 410 helix: 1.57 (0.34), residues: 242 sheet: 0.78 (0.93), residues: 25 loop : 1.25 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.003 0.001 HIS A 396 PHE 0.010 0.001 PHE A 269 TYR 0.007 0.001 TYR A 275 ARG 0.003 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.362 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.0677 time to fit residues: 49.8904 Evaluate side-chains 44 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.130563 restraints weight = 3425.613| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.20 r_work: 0.3002 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3348 Z= 0.130 Angle : 0.453 7.006 4556 Z= 0.234 Chirality : 0.039 0.167 533 Planarity : 0.003 0.030 564 Dihedral : 4.634 30.903 515 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.46 % Allowed : 19.53 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.41), residues: 410 helix: 1.73 (0.34), residues: 243 sheet: 0.94 (0.96), residues: 25 loop : 1.23 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.012 0.001 PHE A 269 TYR 0.012 0.001 TYR A 127 ARG 0.003 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.12 seconds wall clock time: 36 minutes 43.14 seconds (2203.14 seconds total)