Starting phenix.real_space_refine on Sun Mar 10 19:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwl_20923/03_2024/6uwl_20923_updated.pdb" } resolution = 3.62 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1634 atoms to isotropic. 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 1 5.49 5 S 18 5.16 5 C 1998 2.51 5 N 479 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3029 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3029 Unusual residues: {'6OU': 1} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 402, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 384, None: 1} Not linked: pdbres="ASP A 501 " pdbres="6OU A 502 " Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.71 Number of scatterers: 3029 At special positions: 0 Unit cell: (67.84, 67.84, 77.38, 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 18 16.00 P 1 15.00 O 533 8.00 N 479 7.00 C 1998 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 618.9 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 74.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.931A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 69 removed outlier: 4.072A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.590A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 removed outlier: 3.755A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.234A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 219 removed outlier: 3.901A pdb=" N TYR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 229 through 253 removed outlier: 4.843A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 6.153A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.050A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.012A pdb=" N GLY A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 359 through 370 Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.016A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 585 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: 0.79 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 467 1.31 - 1.43: 749 1.43 - 1.56: 1819 1.56 - 1.68: 13 1.68 - 1.81: 35 Bond restraints: 3083 Sorted by residual: bond pdb=" C16 6OU A 502 " pdb=" O18 6OU A 502 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C31 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C39 6OU A 502 " pdb=" C40 6OU A 502 " ideal model delta sigma weight residual 1.497 1.565 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C15 6OU A 502 " pdb=" C16 6OU A 502 " ideal model delta sigma weight residual 1.501 1.558 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" SD FME A 1 " pdb=" CE FME A 1 " ideal model delta sigma weight residual 1.805 1.751 0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.37: 94 106.37 - 112.92: 1686 112.92 - 119.47: 959 119.47 - 126.03: 1420 126.03 - 132.58: 31 Bond angle restraints: 4190 Sorted by residual: angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.81 -11.00 2.21e+00 2.05e-01 2.48e+01 angle pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " pdb=" CG LEU A 228 " ideal model delta sigma weight residual 116.30 132.58 -16.28 3.50e+00 8.16e-02 2.16e+01 angle pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " pdb=" O26 6OU A 502 " ideal model delta sigma weight residual 93.95 107.46 -13.51 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C ILE A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.83e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 121.13 -7.23 1.80e+00 3.09e-01 1.61e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 1708 25.45 - 50.91: 100 50.91 - 76.36: 14 76.36 - 101.81: 0 101.81 - 127.26: 3 Dihedral angle restraints: 1825 sinusoidal: 684 harmonic: 1141 Sorted by residual: dihedral pdb=" CA ILE A 294 " pdb=" C ILE A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta harmonic sigma weight residual 180.00 143.05 36.95 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA PRO A 75 " pdb=" C PRO A 75 " pdb=" N ALA A 76 " pdb=" CA ALA A 76 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA SER A 72 " pdb=" C SER A 72 " pdb=" N ILE A 73 " pdb=" CA ILE A 73 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 357 0.052 - 0.105: 112 0.105 - 0.157: 45 0.157 - 0.209: 9 0.209 - 0.262: 1 Chirality restraints: 524 Sorted by residual: chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 521 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 356 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 45 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 928 2.82 - 3.34: 3017 3.34 - 3.86: 5032 3.86 - 4.38: 5662 4.38 - 4.90: 9692 Nonbonded interactions: 24331 Sorted by model distance: nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.303 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.313 2.440 nonbonded pdb=" O THR A 403 " pdb=" OG1 THR A 407 " model vdw 2.326 2.440 nonbonded pdb=" O ILE A 61 " pdb=" OG SER A 65 " model vdw 2.342 2.440 nonbonded pdb=" O MET A 311 " pdb=" OG SER A 349 " model vdw 2.349 2.440 ... (remaining 24326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 3.460 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.740 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.008 0.086 3083 Z= 0.524 Angle : 1.158 16.279 4190 Z= 0.567 Chirality : 0.060 0.262 524 Planarity : 0.009 0.064 510 Dihedral : 16.853 127.264 1101 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.58 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.71 (0.31), residues: 396 helix: -2.71 (0.20), residues: 321 sheet: None (None), residues: 0 loop : -3.85 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 264 PHE 0.017 0.002 PHE A 248 TYR 0.028 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8103 (m-80) cc_final: 0.7888 (m-80) REVERT: A 337 GLN cc_start: 0.7418 (mm-40) cc_final: 0.5815 (tt0) REVERT: A 362 MET cc_start: 0.8500 (mmm) cc_final: 0.8280 (mmp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1474 time to fit residues: 16.3222 Evaluate side-chains 70 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 40 HIS A 173 ASN A 199 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3083 Z= 0.211 Angle : 0.669 10.204 4190 Z= 0.336 Chirality : 0.042 0.137 524 Planarity : 0.006 0.054 510 Dihedral : 11.678 90.365 463 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.82 % Allowed : 18.79 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.27 (0.39), residues: 396 helix: -0.88 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -3.69 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 332 PHE 0.013 0.001 PHE A 324 TYR 0.018 0.001 TYR A 299 ARG 0.005 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.7995 (m-80) cc_final: 0.7739 (m-80) REVERT: A 227 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 286 MET cc_start: 0.8566 (mtp) cc_final: 0.8359 (mtp) REVERT: A 311 MET cc_start: 0.7661 (mtm) cc_final: 0.7145 (mtt) REVERT: A 337 GLN cc_start: 0.7570 (mm-40) cc_final: 0.6275 (tt0) REVERT: A 362 MET cc_start: 0.8362 (mmm) cc_final: 0.8160 (mmp) REVERT: A 406 LEU cc_start: 0.8949 (mm) cc_final: 0.8609 (mp) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1266 time to fit residues: 13.5514 Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 36 optimal weight: 0.0270 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 12 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3083 Z= 0.163 Angle : 0.635 9.931 4190 Z= 0.311 Chirality : 0.041 0.139 524 Planarity : 0.005 0.051 510 Dihedral : 9.277 74.439 463 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.87 % Allowed : 21.02 % Favored : 76.11 % 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: -1.18 (0.42), residues: 396 helix: -0.08 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -3.84 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 37 PHE 0.010 0.001 PHE A 324 TYR 0.020 0.001 TYR A 299 ARG 0.004 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.7931 (m-80) cc_final: 0.7675 (m-80) REVERT: A 83 VAL cc_start: 0.8392 (m) cc_final: 0.8163 (m) REVERT: A 86 VAL cc_start: 0.9339 (t) cc_final: 0.9111 (m) REVERT: A 275 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 311 MET cc_start: 0.7735 (mtm) cc_final: 0.7324 (mtt) REVERT: A 337 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6122 (tt0) REVERT: A 362 MET cc_start: 0.8368 (mmm) cc_final: 0.8093 (mmm) REVERT: A 390 ASP cc_start: 0.6513 (t0) cc_final: 0.6287 (t0) REVERT: A 406 LEU cc_start: 0.8885 (mm) cc_final: 0.8512 (mt) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.1197 time to fit residues: 13.1024 Evaluate side-chains 78 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 32 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.167 Angle : 0.622 9.993 4190 Z= 0.306 Chirality : 0.041 0.153 524 Planarity : 0.005 0.050 510 Dihedral : 8.249 66.049 463 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.82 % Allowed : 22.93 % Favored : 73.25 % 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: -0.63 (0.43), residues: 396 helix: 0.26 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.68 (0.66), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.021 0.001 PHE A 261 TYR 0.017 0.001 TYR A 299 ARG 0.003 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.7961 (m-80) cc_final: 0.7738 (m-80) REVERT: A 83 VAL cc_start: 0.8325 (m) cc_final: 0.8034 (m) REVERT: A 86 VAL cc_start: 0.9217 (t) cc_final: 0.9010 (m) REVERT: A 286 MET cc_start: 0.8682 (mtp) cc_final: 0.8365 (mtp) REVERT: A 311 MET cc_start: 0.7758 (mtm) cc_final: 0.7331 (mtt) REVERT: A 337 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6303 (tt0) REVERT: A 362 MET cc_start: 0.8388 (mmm) cc_final: 0.8166 (mmm) REVERT: A 390 ASP cc_start: 0.6294 (t0) cc_final: 0.6093 (t70) REVERT: A 406 LEU cc_start: 0.8884 (mm) cc_final: 0.8522 (mt) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1273 time to fit residues: 13.4016 Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 26 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3083 Z= 0.174 Angle : 0.637 9.677 4190 Z= 0.309 Chirality : 0.042 0.158 524 Planarity : 0.004 0.048 510 Dihedral : 7.876 62.750 463 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.82 % Allowed : 24.20 % Favored : 71.97 % 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: -0.42 (0.43), residues: 396 helix: 0.44 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.87 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.015 0.001 PHE A 261 TYR 0.019 0.001 TYR A 299 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7116 (t80) REVERT: A 42 TYR cc_start: 0.7960 (m-80) cc_final: 0.7719 (m-80) REVERT: A 83 VAL cc_start: 0.8272 (m) cc_final: 0.7983 (m) REVERT: A 86 VAL cc_start: 0.9221 (t) cc_final: 0.8997 (m) REVERT: A 286 MET cc_start: 0.8669 (mtp) cc_final: 0.8303 (mtp) REVERT: A 311 MET cc_start: 0.7836 (mtm) cc_final: 0.7432 (mtt) REVERT: A 337 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6251 (tt0) REVERT: A 406 LEU cc_start: 0.8881 (mm) cc_final: 0.8477 (mt) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1287 time to fit residues: 13.1012 Evaluate side-chains 81 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3083 Z= 0.267 Angle : 0.685 9.736 4190 Z= 0.333 Chirality : 0.043 0.144 524 Planarity : 0.005 0.050 510 Dihedral : 8.333 79.339 463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.78 % Allowed : 24.20 % Favored : 71.02 % 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: -0.33 (0.43), residues: 396 helix: 0.59 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -4.29 (0.59), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 37 PHE 0.012 0.001 PHE A 261 TYR 0.024 0.002 TYR A 299 ARG 0.003 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8404 (m) cc_final: 0.8095 (m) REVERT: A 86 VAL cc_start: 0.9269 (t) cc_final: 0.9048 (m) REVERT: A 286 MET cc_start: 0.8749 (mtp) cc_final: 0.8250 (mtp) REVERT: A 311 MET cc_start: 0.7918 (mtm) cc_final: 0.7603 (mtt) REVERT: A 337 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6181 (tt0) outliers start: 15 outliers final: 14 residues processed: 80 average time/residue: 0.1160 time to fit residues: 11.7826 Evaluate side-chains 85 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 19 optimal weight: 0.1980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.188 Angle : 0.651 10.502 4190 Z= 0.311 Chirality : 0.041 0.146 524 Planarity : 0.004 0.044 510 Dihedral : 7.944 72.661 463 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.10 % Allowed : 24.84 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.44), residues: 396 helix: 0.75 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -4.21 (0.59), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.012 0.001 PHE A 261 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.346 Fit side-chains REVERT: A 83 VAL cc_start: 0.8279 (m) cc_final: 0.7960 (m) REVERT: A 86 VAL cc_start: 0.9266 (t) cc_final: 0.9048 (m) REVERT: A 286 MET cc_start: 0.8690 (mtp) cc_final: 0.8318 (mtp) REVERT: A 311 MET cc_start: 0.7902 (mtm) cc_final: 0.7522 (mtt) REVERT: A 337 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6274 (tt0) REVERT: A 406 LEU cc_start: 0.8945 (mm) cc_final: 0.8693 (mt) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.1214 time to fit residues: 12.8931 Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3083 Z= 0.238 Angle : 0.690 11.872 4190 Z= 0.331 Chirality : 0.042 0.157 524 Planarity : 0.004 0.042 510 Dihedral : 8.142 77.917 463 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.10 % Allowed : 27.07 % Favored : 67.83 % 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: 0.01 (0.44), residues: 396 helix: 0.79 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -3.84 (0.64), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.011 0.001 PHE A 261 TYR 0.019 0.002 TYR A 299 ARG 0.003 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8354 (m) cc_final: 0.8052 (m) REVERT: A 86 VAL cc_start: 0.9245 (t) cc_final: 0.9024 (m) REVERT: A 286 MET cc_start: 0.8709 (mtp) cc_final: 0.8214 (mtp) REVERT: A 311 MET cc_start: 0.7904 (mtm) cc_final: 0.7557 (mtt) REVERT: A 337 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6320 (tt0) REVERT: A 406 LEU cc_start: 0.9019 (mm) cc_final: 0.8749 (mt) outliers start: 16 outliers final: 15 residues processed: 80 average time/residue: 0.1168 time to fit residues: 11.7838 Evaluate side-chains 84 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 264 HIS A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.276 Angle : 0.708 11.722 4190 Z= 0.339 Chirality : 0.043 0.161 524 Planarity : 0.005 0.041 510 Dihedral : 8.445 85.256 463 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.73 % Allowed : 26.43 % Favored : 67.83 % 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: -0.06 (0.44), residues: 396 helix: 0.76 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -3.91 (0.64), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.010 0.001 PHE A 261 TYR 0.022 0.002 TYR A 299 ARG 0.004 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8120 (m) cc_final: 0.7819 (m) REVERT: A 85 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 86 VAL cc_start: 0.9252 (t) cc_final: 0.9034 (m) REVERT: A 286 MET cc_start: 0.8743 (mtp) cc_final: 0.8248 (mtp) REVERT: A 311 MET cc_start: 0.7886 (mtm) cc_final: 0.7569 (mtt) REVERT: A 337 GLN cc_start: 0.7363 (mm110) cc_final: 0.6218 (tt0) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.1185 time to fit residues: 12.0520 Evaluate side-chains 82 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.235 Angle : 0.694 12.316 4190 Z= 0.330 Chirality : 0.043 0.163 524 Planarity : 0.004 0.041 510 Dihedral : 8.318 82.964 463 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.10 % Allowed : 28.03 % Favored : 66.88 % 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: 0.04 (0.44), residues: 396 helix: 0.83 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -3.88 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.011 0.001 PHE A 261 TYR 0.021 0.002 TYR A 299 ARG 0.004 0.001 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8106 (m) cc_final: 0.7807 (m) REVERT: A 286 MET cc_start: 0.8771 (mtp) cc_final: 0.8299 (mtp) REVERT: A 311 MET cc_start: 0.7861 (mtm) cc_final: 0.7512 (mtt) REVERT: A 337 GLN cc_start: 0.7514 (mm110) cc_final: 0.6402 (tt0) REVERT: A 406 LEU cc_start: 0.8993 (mm) cc_final: 0.8717 (mt) outliers start: 16 outliers final: 15 residues processed: 77 average time/residue: 0.1196 time to fit residues: 11.6582 Evaluate side-chains 82 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099396 restraints weight = 5801.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101787 restraints weight = 3207.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103207 restraints weight = 2280.849| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.220 Angle : 0.700 12.639 4190 Z= 0.332 Chirality : 0.043 0.186 524 Planarity : 0.004 0.040 510 Dihedral : 8.175 79.413 463 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.46 % Allowed : 29.30 % Favored : 66.24 % 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: 0.06 (0.44), residues: 396 helix: 0.79 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -3.74 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.011 0.001 PHE A 261 TYR 0.020 0.002 TYR A 299 ARG 0.005 0.001 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1107.02 seconds wall clock time: 20 minutes 32.14 seconds (1232.14 seconds total)