Starting phenix.real_space_refine on Fri Apr 5 14:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/04_2024/8hj3_34831_neut_updated.pdb" } resolution = 3.29 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3274 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 419 "'] Classifications: {'peptide': 416, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395, None: 1} Not linked: pdbres="LYS A 419 " pdbres="NAP A 501 " Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 2.42, per 1000 atoms: 0.74 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 71.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 1.37 Conformation dependent library (CDL) restraints added in 801.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 48.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 4.117A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.774A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.654A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.599A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.482A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.418A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.970A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 167 hydrogen bonds defined for protein. 486 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: 0.94 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1062 1.34 - 1.46: 724 1.46 - 1.58: 1533 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" N LYS A 389 " pdb=" CA LYS A 389 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.61e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" N HIS A 388 " pdb=" CA HIS A 388 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.37e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.24: 64 104.24 - 111.68: 1575 111.68 - 119.12: 1183 119.12 - 126.55: 1667 126.55 - 133.99: 72 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C TRP A 89 " pdb=" N MET A 90 " pdb=" CA MET A 90 " ideal model delta sigma weight residual 121.58 114.33 7.25 1.95e+00 2.63e-01 1.38e+01 angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 106.80 7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N MET A 90 " pdb=" CA MET A 90 " pdb=" CB MET A 90 " ideal model delta sigma weight residual 110.41 116.33 -5.92 1.68e+00 3.54e-01 1.24e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 115.58 -4.71 1.54e+00 4.22e-01 9.37e+00 angle pdb=" CA MET A 90 " pdb=" CB MET A 90 " pdb=" CG MET A 90 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.01e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1829 17.65 - 35.29: 154 35.29 - 52.94: 38 52.94 - 70.59: 7 70.59 - 88.23: 4 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 90 " pdb=" C MET A 90 " pdb=" N THR A 91 " pdb=" CA THR A 91 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -88.23 88.23 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 346 0.040 - 0.081: 99 0.081 - 0.121: 55 0.121 - 0.161: 0 0.161 - 0.202: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA MET A 90 " pdb=" N MET A 90 " pdb=" C MET A 90 " pdb=" CB MET A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " 0.053 2.00e-02 2.50e+03 7.24e-02 1.05e+02 pdb=" C2N NAP A 501 " -0.128 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.046 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.036 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 142 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 197 " -0.013 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE A 197 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 197 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 197 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 197 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 197 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 197 " -0.000 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 362 2.74 - 3.28: 3497 3.28 - 3.82: 5991 3.82 - 4.36: 6980 4.36 - 4.90: 11719 Nonbonded interactions: 28549 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" NE2 GLN A 337 " model vdw 2.200 2.520 nonbonded pdb=" NH1 ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.253 2.520 nonbonded pdb=" O TYR A 20 " pdb=" NZ LYS A 391 " model vdw 2.264 2.520 nonbonded pdb=" O ILE A 309 " pdb=" NZ LYS A 333 " model vdw 2.286 2.520 nonbonded pdb=" N GLU A 325 " pdb=" OE1 GLU A 325 " model vdw 2.298 2.520 ... (remaining 28544 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.600 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 3351 Z= 0.378 Angle : 0.802 7.569 4561 Z= 0.454 Chirality : 0.046 0.202 501 Planarity : 0.005 0.072 579 Dihedral : 14.797 88.231 1274 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % 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: 1.21 (0.42), residues: 414 helix: 1.79 (0.35), residues: 206 sheet: 0.24 (0.68), residues: 64 loop : -0.31 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 92 HIS 0.002 0.001 HIS A 61 PHE 0.035 0.003 PHE A 197 TYR 0.013 0.001 TYR A 132 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6792 (t70) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1329 time to fit residues: 11.0627 Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.202 Angle : 0.544 8.535 4561 Z= 0.287 Chirality : 0.044 0.189 501 Planarity : 0.004 0.052 579 Dihedral : 8.736 63.896 519 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.91 % Allowed : 9.70 % Favored : 89.39 % 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: 1.27 (0.41), residues: 414 helix: 1.96 (0.35), residues: 205 sheet: 0.30 (0.67), residues: 64 loop : -0.47 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.002 0.001 HIS A 388 PHE 0.050 0.003 PHE A 197 TYR 0.006 0.001 TYR A 385 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8058 (tp30) cc_final: 0.7749 (tp30) REVERT: A 29 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 197 PHE cc_start: 0.8439 (m-80) cc_final: 0.8148 (m-80) REVERT: A 388 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6534 (t70) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 0.1251 time to fit residues: 10.2906 Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3351 Z= 0.307 Angle : 0.594 8.592 4561 Z= 0.312 Chirality : 0.044 0.202 501 Planarity : 0.004 0.053 579 Dihedral : 8.576 59.466 519 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 12.42 % Favored : 85.15 % 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: 1.07 (0.41), residues: 414 helix: 1.85 (0.35), residues: 206 sheet: 0.04 (0.67), residues: 66 loop : -0.63 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 89 HIS 0.004 0.001 HIS A 388 PHE 0.035 0.003 PHE A 197 TYR 0.010 0.001 TYR A 147 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6983 (m-10) cc_final: 0.6745 (m-10) REVERT: A 25 GLU cc_start: 0.8163 (tp30) cc_final: 0.7879 (tp30) REVERT: A 29 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 193 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8705 (tp40) REVERT: A 197 PHE cc_start: 0.8445 (m-80) cc_final: 0.8207 (m-80) REVERT: A 388 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6486 (t70) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1261 time to fit residues: 9.7841 Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.193 Angle : 0.525 8.777 4561 Z= 0.277 Chirality : 0.043 0.205 501 Planarity : 0.004 0.050 579 Dihedral : 7.991 59.996 519 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.73 % Allowed : 13.03 % Favored : 84.24 % 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: 1.20 (0.41), residues: 414 helix: 2.03 (0.35), residues: 204 sheet: 0.08 (0.68), residues: 66 loop : -0.63 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.029 0.002 PHE A 197 TYR 0.008 0.001 TYR A 147 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.7033 (m-10) cc_final: 0.6778 (m-10) REVERT: A 21 MET cc_start: 0.7653 (ptp) cc_final: 0.7145 (ptp) REVERT: A 29 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 388 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.6251 (t70) REVERT: A 395 MET cc_start: 0.7505 (mmm) cc_final: 0.7238 (mmt) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.1270 time to fit residues: 11.1045 Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3351 Z= 0.292 Angle : 0.585 8.899 4561 Z= 0.309 Chirality : 0.045 0.211 501 Planarity : 0.004 0.051 579 Dihedral : 7.753 55.862 519 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 14.55 % Favored : 82.73 % 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: 1.03 (0.41), residues: 414 helix: 1.88 (0.35), residues: 204 sheet: -0.10 (0.68), residues: 66 loop : -0.63 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.018 0.002 PHE A 341 TYR 0.012 0.001 TYR A 160 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.7123 (m-10) cc_final: 0.6784 (m-10) REVERT: A 21 MET cc_start: 0.7651 (ptp) cc_final: 0.7172 (ptp) REVERT: A 25 GLU cc_start: 0.8101 (tp30) cc_final: 0.7621 (tp30) REVERT: A 29 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 388 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6534 (t70) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.1237 time to fit residues: 9.6998 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.211 Angle : 0.562 9.350 4561 Z= 0.296 Chirality : 0.044 0.219 501 Planarity : 0.004 0.050 579 Dihedral : 7.521 58.538 519 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.64 % Allowed : 14.24 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.41), residues: 414 helix: 1.88 (0.35), residues: 204 sheet: -0.26 (0.66), residues: 66 loop : -0.63 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.003 0.001 HIS A 267 PHE 0.021 0.002 PHE A 341 TYR 0.012 0.001 TYR A 160 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7581 (ptp) cc_final: 0.7102 (ptp) REVERT: A 25 GLU cc_start: 0.8073 (tp30) cc_final: 0.7682 (tp30) REVERT: A 29 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 388 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6304 (t70) REVERT: A 395 MET cc_start: 0.7507 (mmm) cc_final: 0.7243 (mmt) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1289 time to fit residues: 10.1824 Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3351 Z= 0.267 Angle : 0.596 9.882 4561 Z= 0.314 Chirality : 0.045 0.220 501 Planarity : 0.004 0.050 579 Dihedral : 7.279 54.469 519 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 14.24 % Favored : 82.42 % 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: 0.86 (0.41), residues: 414 helix: 1.69 (0.35), residues: 209 sheet: -0.26 (0.66), residues: 66 loop : -0.67 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.004 0.001 HIS A 267 PHE 0.020 0.002 PHE A 341 TYR 0.009 0.001 TYR A 132 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7619 (ptp) cc_final: 0.7163 (ptp) REVERT: A 25 GLU cc_start: 0.8148 (tp30) cc_final: 0.7794 (tp30) REVERT: A 29 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 388 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.6374 (t70) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.1265 time to fit residues: 9.6664 Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS 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: 1.9990 chunk 3 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.209 Angle : 0.592 10.851 4561 Z= 0.311 Chirality : 0.044 0.216 501 Planarity : 0.004 0.049 579 Dihedral : 6.845 49.565 519 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.94 % Allowed : 14.24 % Favored : 81.82 % 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: 0.96 (0.42), residues: 414 helix: 1.77 (0.35), residues: 209 sheet: -0.12 (0.67), residues: 66 loop : -0.68 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.001 HIS A 267 PHE 0.018 0.002 PHE A 341 TYR 0.007 0.001 TYR A 132 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7557 (ptp) cc_final: 0.7038 (ptp) REVERT: A 25 GLU cc_start: 0.8147 (tp30) cc_final: 0.7819 (tp30) REVERT: A 29 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 90 MET cc_start: 0.7451 (pmm) cc_final: 0.7209 (pmm) REVERT: A 388 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6328 (t70) REVERT: A 395 MET cc_start: 0.7574 (mmm) cc_final: 0.7287 (mmt) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.1156 time to fit residues: 10.0335 Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3351 Z= 0.297 Angle : 0.642 9.796 4561 Z= 0.337 Chirality : 0.047 0.209 501 Planarity : 0.005 0.049 579 Dihedral : 6.854 46.172 519 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.64 % Allowed : 15.45 % Favored : 80.91 % 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: 0.77 (0.42), residues: 414 helix: 1.59 (0.35), residues: 208 sheet: -0.22 (0.67), residues: 66 loop : -0.71 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.008 0.002 HIS A 75 PHE 0.019 0.002 PHE A 341 TYR 0.009 0.001 TYR A 132 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8176 (tp30) cc_final: 0.7943 (tp30) outliers start: 12 outliers final: 12 residues processed: 61 average time/residue: 0.1256 time to fit residues: 9.8945 Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3351 Z= 0.222 Angle : 0.632 11.011 4561 Z= 0.330 Chirality : 0.045 0.213 501 Planarity : 0.004 0.048 579 Dihedral : 6.524 42.314 519 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.64 % Allowed : 15.15 % Favored : 81.21 % 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: 0.84 (0.42), residues: 414 helix: 1.65 (0.35), residues: 209 sheet: -0.06 (0.68), residues: 66 loop : -0.78 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.003 0.001 HIS A 267 PHE 0.021 0.002 PHE A 197 TYR 0.008 0.001 TYR A 132 ARG 0.001 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7440 (pmm) cc_final: 0.6833 (pmm) outliers start: 12 outliers final: 12 residues processed: 63 average time/residue: 0.1374 time to fit residues: 10.9702 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 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 = 0.4041 r_free = 0.4041 target = 0.141589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122548 restraints weight = 8127.582| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.78 r_work: 0.3612 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3351 Z= 0.262 Angle : 0.658 10.629 4561 Z= 0.341 Chirality : 0.045 0.215 501 Planarity : 0.004 0.048 579 Dihedral : 6.472 40.398 519 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.64 % Allowed : 15.76 % Favored : 80.61 % 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: 0.82 (0.42), residues: 414 helix: 1.64 (0.35), residues: 209 sheet: -0.03 (0.68), residues: 66 loop : -0.80 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.004 0.001 HIS A 267 PHE 0.019 0.002 PHE A 341 TYR 0.015 0.001 TYR A 160 ARG 0.002 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.10 seconds wall clock time: 21 minutes 11.39 seconds (1271.39 seconds total)