Starting phenix.real_space_refine on Mon May 6 15:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8t_19009/05_2024/8r8t_19009_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8t_19009/05_2024/8r8t_19009.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/8r8t_19009/05_2024/8r8t_19009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8t_19009/05_2024/8r8t_19009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8t_19009/05_2024/8r8t_19009_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8t_19009/05_2024/8r8t_19009_updated.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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2164 2.51 5 N 505 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3252 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.71 Number of scatterers: 3256 At special positions: 0 Unit cell: (80.22, 56.154, 66.468, 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 18 16.00 O 569 8.00 N 505 7.00 C 2164 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: 1.38 Conformation dependent library (CDL) restraints added in 598.0 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 80.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 105 through 126 removed outlier: 3.639A pdb=" N LEU A 111 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 120 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 4.048A pdb=" N GLY A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.995A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.071A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix removed outlier: 3.516A pdb=" N ASP A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 Processing helix chain 'A' and resid 200 through 218 removed outlier: 3.781A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 234 through 259 removed outlier: 3.515A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 267 through 295 Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.510A pdb=" N ASP A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 332 through 362 removed outlier: 5.025A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 387 Processing helix chain 'A' and resid 398 through 422 removed outlier: 4.944A pdb=" N ASP A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 removed outlier: 3.643A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 4.000A pdb=" N GLU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 509 Proline residue: A 490 - end of helix removed outlier: 3.583A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 660 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: 0.87 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 962 1.34 - 1.46: 540 1.46 - 1.58: 1807 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3337 Sorted by residual: bond pdb=" O ETA A 601 " pdb=" CB ETA A 601 " ideal model delta sigma weight residual 1.413 1.460 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" N GLU A 448 " pdb=" CA GLU A 448 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.33e-02 5.65e+03 4.45e+00 bond pdb=" CA ETA A 601 " pdb=" CB ETA A 601 " ideal model delta sigma weight residual 1.513 1.545 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C GLU A 448 " pdb=" O GLU A 448 " ideal model delta sigma weight residual 1.236 1.221 0.014 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C TYR A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 ... (remaining 3332 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 89 107.14 - 113.85: 1890 113.85 - 120.57: 1441 120.57 - 127.28: 1095 127.28 - 133.99: 35 Bond angle restraints: 4550 Sorted by residual: angle pdb=" CB MET A 344 " pdb=" CG MET A 344 " pdb=" SD MET A 344 " ideal model delta sigma weight residual 112.70 119.32 -6.62 3.00e+00 1.11e-01 4.87e+00 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 109.81 114.53 -4.72 2.21e+00 2.05e-01 4.57e+00 angle pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.70e+00 3.46e-01 4.18e+00 angle pdb=" N GLU A 448 " pdb=" CA GLU A 448 " pdb=" C GLU A 448 " ideal model delta sigma weight residual 112.54 110.07 2.47 1.22e+00 6.72e-01 4.09e+00 angle pdb=" N PRO A 256 " pdb=" CA PRO A 256 " pdb=" C PRO A 256 " ideal model delta sigma weight residual 110.70 113.14 -2.44 1.22e+00 6.72e-01 4.01e+00 ... (remaining 4545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 1701 17.63 - 35.27: 173 35.27 - 52.90: 36 52.90 - 70.53: 8 70.53 - 88.16: 5 Dihedral angle restraints: 1923 sinusoidal: 720 harmonic: 1203 Sorted by residual: dihedral pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " pdb=" OD1 ASN A 331 " ideal model delta sinusoidal sigma weight residual 120.00 -170.36 -69.64 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " pdb=" CD GLU A 318 " pdb=" OE1 GLU A 318 " ideal model delta sinusoidal sigma weight residual 0.00 88.16 -88.16 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 1920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 352 0.027 - 0.055: 118 0.055 - 0.082: 55 0.082 - 0.109: 17 0.109 - 0.137: 2 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.30 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA LEU A 220 " pdb=" N LEU A 220 " pdb=" C LEU A 220 " pdb=" CB LEU A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.69e-01 ... (remaining 541 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 448 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C GLU A 448 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 448 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 449 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 444 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 303 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 304 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.018 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 338 2.75 - 3.28: 3467 3.28 - 3.82: 5655 3.82 - 4.36: 6850 4.36 - 4.90: 11533 Nonbonded interactions: 27843 Sorted by model distance: nonbonded pdb=" N GLU A 367 " pdb=" OE1 GLU A 367 " model vdw 2.207 2.520 nonbonded pdb=" O GLN A 357 " pdb=" OG1 THR A 361 " model vdw 2.280 2.440 nonbonded pdb=" O THR A 263 " pdb=" OG1 THR A 263 " model vdw 2.322 2.440 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 2.343 2.440 nonbonded pdb=" O PRO A 490 " pdb=" ND2 ASN A 494 " model vdw 2.347 2.520 ... (remaining 27838 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: 0.120 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: 0.930 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.080 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.002 0.047 3337 Z= 0.165 Angle : 0.529 6.620 4550 Z= 0.267 Chirality : 0.035 0.137 544 Planarity : 0.004 0.041 552 Dihedral : 15.728 88.164 1157 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 17.51 % Favored : 82.49 % 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: 1.06 (0.41), residues: 416 helix: 1.32 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.51 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 391 HIS 0.001 0.000 HIS A 145 PHE 0.018 0.001 PHE A 502 TYR 0.015 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.375 Fit side-chains REVERT: A 311 LEU cc_start: 0.6049 (mm) cc_final: 0.5750 (tp) REVERT: A 448 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7732 (mm-30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.9948 time to fit residues: 49.6612 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3337 Z= 0.244 Angle : 0.591 6.723 4550 Z= 0.300 Chirality : 0.040 0.131 544 Planarity : 0.005 0.037 552 Dihedral : 4.369 17.015 449 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.67 % Allowed : 13.28 % Favored : 83.05 % 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: 1.61 (0.42), residues: 416 helix: 1.64 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.25 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 391 HIS 0.003 0.001 HIS A 145 PHE 0.017 0.002 PHE A 502 TYR 0.016 0.001 TYR A 117 ARG 0.002 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.312 Fit side-chains REVERT: A 390 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5048 (mm) REVERT: A 406 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: A 448 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7529 (mt-10) outliers start: 13 outliers final: 4 residues processed: 57 average time/residue: 0.9042 time to fit residues: 53.6263 Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3337 Z= 0.203 Angle : 0.554 6.843 4550 Z= 0.278 Chirality : 0.038 0.127 544 Planarity : 0.004 0.036 552 Dihedral : 4.308 17.059 449 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.95 % Allowed : 14.41 % Favored : 81.64 % 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: 1.63 (0.42), residues: 416 helix: 1.69 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.41 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 391 HIS 0.001 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.409 Fit side-chains REVERT: A 218 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7635 (tp) REVERT: A 366 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 406 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: A 448 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7451 (mt-10) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 0.8916 time to fit residues: 53.0578 Evaluate side-chains 50 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.0020 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3337 Z= 0.168 Angle : 0.530 6.332 4550 Z= 0.263 Chirality : 0.037 0.132 544 Planarity : 0.004 0.035 552 Dihedral : 4.195 16.756 449 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.39 % Allowed : 14.97 % Favored : 81.64 % 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: 1.81 (0.42), residues: 416 helix: 1.85 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.54 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 391 HIS 0.000 0.000 HIS A 145 PHE 0.015 0.001 PHE A 502 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.401 Fit side-chains REVERT: A 218 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7672 (tp) REVERT: A 298 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 406 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: A 419 THR cc_start: 0.8207 (p) cc_final: 0.7977 (p) REVERT: A 448 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7338 (mt-10) outliers start: 12 outliers final: 3 residues processed: 59 average time/residue: 0.9852 time to fit residues: 60.4369 Evaluate side-chains 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3337 Z= 0.218 Angle : 0.565 6.756 4550 Z= 0.280 Chirality : 0.038 0.135 544 Planarity : 0.004 0.037 552 Dihedral : 4.271 16.752 449 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.95 % Allowed : 15.82 % Favored : 80.23 % 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: 1.73 (0.42), residues: 416 helix: 1.80 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.61 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 391 HIS 0.001 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.017 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.343 Fit side-chains REVERT: A 302 TYR cc_start: 0.8165 (m-80) cc_final: 0.7870 (m-10) REVERT: A 382 MET cc_start: 0.8586 (mtp) cc_final: 0.8378 (mtt) REVERT: A 406 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: A 448 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7376 (mt-10) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 0.8678 time to fit residues: 48.9271 Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.0470 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3337 Z= 0.165 Angle : 0.534 6.516 4550 Z= 0.263 Chirality : 0.037 0.133 544 Planarity : 0.004 0.035 552 Dihedral : 4.182 16.964 449 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.82 % Allowed : 17.23 % Favored : 79.94 % 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 (0.42), residues: 416 helix: 1.89 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.50 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.384 Fit side-chains REVERT: A 218 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7679 (tp) REVERT: A 302 TYR cc_start: 0.8164 (m-80) cc_final: 0.7871 (m-10) REVERT: A 382 MET cc_start: 0.8574 (mtp) cc_final: 0.8372 (mtt) REVERT: A 406 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: A 419 THR cc_start: 0.8223 (p) cc_final: 0.7990 (p) REVERT: A 448 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7349 (mt-10) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.7412 time to fit residues: 41.2977 Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0870 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3337 Z= 0.162 Angle : 0.536 7.190 4550 Z= 0.263 Chirality : 0.037 0.129 544 Planarity : 0.004 0.035 552 Dihedral : 4.122 16.636 449 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 17.80 % Favored : 79.10 % 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: 1.97 (0.42), residues: 416 helix: 1.96 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.49 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 PHE 0.017 0.001 PHE A 502 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.442 Fit side-chains REVERT: A 218 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7673 (tp) REVERT: A 302 TYR cc_start: 0.8228 (m-80) cc_final: 0.7926 (m-10) REVERT: A 398 TYR cc_start: 0.7831 (m-80) cc_final: 0.7587 (m-80) REVERT: A 406 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 418 PHE cc_start: 0.8215 (m-80) cc_final: 0.7728 (m-80) REVERT: A 419 THR cc_start: 0.8224 (p) cc_final: 0.7988 (p) REVERT: A 448 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7271 (mt-10) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.8099 time to fit residues: 44.2320 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 406 TYR 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: 2.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3337 Z= 0.220 Angle : 0.573 7.863 4550 Z= 0.282 Chirality : 0.039 0.130 544 Planarity : 0.004 0.036 552 Dihedral : 4.244 16.763 449 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 18.64 % Favored : 78.25 % 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: 1.76 (0.42), residues: 416 helix: 1.83 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.66 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.391 Fit side-chains REVERT: A 302 TYR cc_start: 0.8302 (m-80) cc_final: 0.8009 (m-10) REVERT: A 406 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: A 448 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7283 (mm-30) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.8140 time to fit residues: 41.0110 Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 406 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3337 Z= 0.197 Angle : 0.571 7.460 4550 Z= 0.278 Chirality : 0.038 0.132 544 Planarity : 0.004 0.036 552 Dihedral : 4.251 17.064 449 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 19.49 % Favored : 78.25 % 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: 1.79 (0.42), residues: 416 helix: 1.83 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.55 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.019 0.001 PHE A 502 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.374 Fit side-chains REVERT: A 302 TYR cc_start: 0.8300 (m-80) cc_final: 0.8001 (m-10) REVERT: A 398 TYR cc_start: 0.7865 (m-80) cc_final: 0.7608 (m-80) REVERT: A 406 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: A 448 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7244 (mm-30) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.8326 time to fit residues: 40.1341 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 406 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3337 Z= 0.166 Angle : 0.551 7.251 4550 Z= 0.268 Chirality : 0.037 0.132 544 Planarity : 0.004 0.035 552 Dihedral : 4.136 16.652 449 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 19.49 % Favored : 78.25 % 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: 1.97 (0.42), residues: 416 helix: 1.97 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.56 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.017 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.383 Fit side-chains REVERT: A 406 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: A 419 THR cc_start: 0.8340 (p) cc_final: 0.8110 (p) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.8588 time to fit residues: 43.2586 Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** 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 = 0.3471 r_free = 0.3471 target = 0.130013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103745 restraints weight = 4246.416| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.69 r_work: 0.3032 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3337 Z= 0.179 Angle : 0.572 8.737 4550 Z= 0.276 Chirality : 0.038 0.131 544 Planarity : 0.004 0.035 552 Dihedral : 4.156 16.568 449 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % Favored : 77.97 % 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: 1.85 (0.42), residues: 416 helix: 1.87 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.58 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 PHE 0.021 0.001 PHE A 502 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.73 seconds wall clock time: 27 minutes 7.11 seconds (1627.11 seconds total)