Starting phenix.real_space_refine on Fri Aug 2 16:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcw_38257/08_2024/8xcw_38257_neut.cif" } resolution = 2.87 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 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 2118 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3347 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3272 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3320 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 75 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 17} Link IDs: {None: 18} Time building chain proxies: 4.30, per 1000 atoms: 1.28 Number of scatterers: 3347 At special positions: 0 Unit cell: (67.68, 72.944, 72.192, 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 648 8.00 N 564 7.00 C 2118 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: 1.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.521A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.801A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.687A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.353A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 536 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: 0.98 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.45: 440 1.45 - 1.57: 1887 1.57 - 1.69: 3 1.69 - 1.80: 27 Bond restraints: 3409 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.613 -0.089 1.26e-02 6.30e+03 5.04e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 4.97e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.83e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.21e+01 bond pdb=" C1 AKG A 501 " pdb=" C2 AKG A 501 " ideal model delta sigma weight residual 1.559 1.459 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 95.93 - 103.56: 55 103.56 - 111.19: 1376 111.19 - 118.82: 1388 118.82 - 126.44: 1733 126.44 - 134.07: 82 Bond angle restraints: 4634 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.52 -22.11 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.14 -15.30 1.91e+00 2.73e-01 6.39e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.47 -14.73 1.95e+00 2.62e-01 5.69e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.54 7.92 1.17e+00 7.36e-01 4.61e+01 angle pdb=" N TRP A 89 " pdb=" CA BTRP A 89 " pdb=" C TRP A 89 " ideal model delta sigma weight residual 111.14 104.62 6.52 1.08e+00 8.57e-01 3.64e+01 ... (remaining 4629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 1872 25.02 - 50.04: 123 50.04 - 75.05: 16 75.05 - 100.07: 3 100.07 - 125.09: 1 Dihedral angle restraints: 2015 sinusoidal: 822 harmonic: 1193 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 49.95 125.09 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CB GLU A 8 " pdb=" CG GLU A 8 " pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sinusoidal sigma weight residual 0.00 -88.42 88.42 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" N SER A 351 " pdb=" CA SER A 351 " pdb=" CB SER A 351 " pdb=" OG SER A 351 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 443 0.078 - 0.157: 51 0.157 - 0.235: 1 0.235 - 0.313: 4 0.313 - 0.392: 3 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.35 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 499 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.103 2.00e-02 2.50e+03 1.98e-01 3.90e+02 pdb=" C5N NDP A 500 " 0.255 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.261 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 244 " -0.018 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C ASP A 244 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A 244 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 245 " -0.019 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1198 2.87 - 3.38: 3282 3.38 - 3.89: 5935 3.89 - 4.39: 6843 4.39 - 4.90: 11313 Nonbonded interactions: 28571 Sorted by model distance: nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.363 3.120 nonbonded pdb=" O ASN A 344 " pdb=" OD1 ASN A 344 " model vdw 2.395 3.040 nonbonded pdb=" O PRO A 34 " pdb=" O HOH A 601 " model vdw 2.452 3.040 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.453 3.040 nonbonded pdb=" O PRO A 76 " pdb=" O HOH A 602 " model vdw 2.458 3.040 ... (remaining 28566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.009 0.264 3409 Z= 0.619 Angle : 1.103 22.112 4634 Z= 0.570 Chirality : 0.058 0.392 502 Planarity : 0.010 0.198 591 Dihedral : 16.211 125.090 1255 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.54 % Allowed : 2.95 % Favored : 93.51 % 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: 1.28 (0.43), residues: 415 helix: 2.03 (0.35), residues: 211 sheet: -0.53 (0.79), residues: 48 loop : -0.27 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 263 HIS 0.001 0.000 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.429 Fit side-chains REVERT: A 310 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8743 (mttp) REVERT: A 371 GLU cc_start: 0.7470 (tp30) cc_final: 0.7229 (mm-30) outliers start: 10 outliers final: 2 residues processed: 71 average time/residue: 1.6748 time to fit residues: 121.4310 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 351 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 234 GLN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3409 Z= 0.173 Angle : 0.471 4.671 4634 Z= 0.250 Chirality : 0.042 0.127 502 Planarity : 0.004 0.043 591 Dihedral : 8.530 123.373 475 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.77 % Allowed : 13.27 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 415 helix: 2.48 (0.35), residues: 212 sheet: -0.05 (0.80), residues: 50 loop : -0.21 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.001 0.001 HIS A 61 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.006 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.389 Fit side-chains REVERT: A 12 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7391 (mttt) REVERT: A 13 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7175 (mm-40) REVERT: A 382 TRP cc_start: 0.8803 (m100) cc_final: 0.8518 (m100) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 1.6281 time to fit residues: 88.3141 Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3409 Z= 0.169 Angle : 0.456 5.503 4634 Z= 0.240 Chirality : 0.042 0.125 502 Planarity : 0.004 0.042 591 Dihedral : 7.611 121.950 468 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 14.75 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.43), residues: 415 helix: 2.62 (0.35), residues: 212 sheet: 0.12 (0.67), residues: 70 loop : -0.10 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.002 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.390 Fit side-chains REVERT: A 371 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 382 TRP cc_start: 0.8807 (m100) cc_final: 0.8466 (m100) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 1.6490 time to fit residues: 86.0891 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3409 Z= 0.138 Angle : 0.442 4.939 4634 Z= 0.232 Chirality : 0.041 0.126 502 Planarity : 0.004 0.042 591 Dihedral : 7.286 120.597 468 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.47 % Allowed : 16.52 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 415 helix: 2.67 (0.35), residues: 212 sheet: 0.11 (0.67), residues: 70 loop : -0.15 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.002 0.000 HIS A 394 PHE 0.007 0.001 PHE A 381 TYR 0.004 0.001 TYR A 225 ARG 0.009 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 332 GLU cc_start: 0.8101 (tp30) cc_final: 0.7822 (tp30) REVERT: A 375 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8632 (mptt) REVERT: A 382 TRP cc_start: 0.8678 (m100) cc_final: 0.8371 (m100) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 1.4122 time to fit residues: 78.2506 Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3409 Z= 0.157 Angle : 0.451 5.128 4634 Z= 0.242 Chirality : 0.042 0.127 502 Planarity : 0.004 0.042 591 Dihedral : 7.132 117.982 468 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 17.40 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.43), residues: 415 helix: 2.62 (0.35), residues: 212 sheet: -0.18 (0.72), residues: 62 loop : -0.12 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.001 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.393 Fit side-chains REVERT: A 12 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7216 (mttt) REVERT: A 332 GLU cc_start: 0.8109 (tp30) cc_final: 0.7825 (tp30) REVERT: A 370 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: A 382 TRP cc_start: 0.8727 (m100) cc_final: 0.8381 (m100) outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 1.6405 time to fit residues: 82.3934 Evaluate side-chains 47 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3409 Z= 0.183 Angle : 0.464 5.304 4634 Z= 0.246 Chirality : 0.042 0.126 502 Planarity : 0.005 0.057 591 Dihedral : 7.071 114.123 468 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.77 % Allowed : 17.11 % Favored : 81.12 % 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: 1.98 (0.43), residues: 415 helix: 2.61 (0.35), residues: 212 sheet: 0.12 (0.67), residues: 70 loop : -0.13 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.011 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 382 TRP cc_start: 0.8816 (m100) cc_final: 0.8549 (m100) outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 1.6375 time to fit residues: 82.1759 Evaluate side-chains 46 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3409 Z= 0.160 Angle : 0.452 5.401 4634 Z= 0.240 Chirality : 0.042 0.126 502 Planarity : 0.004 0.043 591 Dihedral : 6.854 108.112 468 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 17.40 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.43), residues: 415 helix: 2.64 (0.35), residues: 212 sheet: 0.11 (0.67), residues: 70 loop : -0.17 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.009 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.344 Fit side-chains REVERT: A 218 GLN cc_start: 0.8793 (tt0) cc_final: 0.8582 (tt0) REVERT: A 371 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 375 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8632 (mptt) REVERT: A 382 TRP cc_start: 0.8766 (m100) cc_final: 0.8496 (m100) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 1.5639 time to fit residues: 81.7101 Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3409 Z= 0.155 Angle : 0.457 5.812 4634 Z= 0.242 Chirality : 0.041 0.126 502 Planarity : 0.005 0.056 591 Dihedral : 6.403 94.368 468 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 18.88 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.43), residues: 415 helix: 2.64 (0.35), residues: 212 sheet: -0.23 (0.72), residues: 62 loop : -0.13 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.001 0.000 HIS A 394 PHE 0.007 0.001 PHE A 381 TYR 0.005 0.001 TYR A 363 ARG 0.015 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8761 (tt0) cc_final: 0.8526 (tt0) REVERT: A 371 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 375 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8609 (mptt) REVERT: A 382 TRP cc_start: 0.8724 (m100) cc_final: 0.8453 (m100) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 1.5211 time to fit residues: 74.9244 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3409 Z= 0.179 Angle : 0.467 5.802 4634 Z= 0.249 Chirality : 0.042 0.126 502 Planarity : 0.004 0.043 591 Dihedral : 5.983 75.069 468 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 17.99 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.43), residues: 415 helix: 2.65 (0.35), residues: 212 sheet: -0.29 (0.71), residues: 62 loop : -0.10 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.009 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 371 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 375 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8593 (mptt) REVERT: A 382 TRP cc_start: 0.8789 (m100) cc_final: 0.8487 (m100) outliers start: 5 outliers final: 1 residues processed: 50 average time/residue: 1.5380 time to fit residues: 78.9171 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 6 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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3409 Z= 0.166 Angle : 0.471 5.831 4634 Z= 0.248 Chirality : 0.042 0.126 502 Planarity : 0.005 0.063 591 Dihedral : 5.789 66.177 468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.88 % Allowed : 19.76 % Favored : 79.35 % 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: 1.94 (0.43), residues: 415 helix: 2.67 (0.35), residues: 212 sheet: -0.29 (0.72), residues: 62 loop : -0.09 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.001 0.000 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.014 0.001 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 371 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 375 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8625 (mptt) REVERT: A 382 TRP cc_start: 0.8750 (m100) cc_final: 0.8456 (m100) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 1.6970 time to fit residues: 81.7414 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.081914 restraints weight = 6856.832| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 1.97 r_work: 0.2555 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3409 Z= 0.216 Angle : 0.499 7.752 4634 Z= 0.263 Chirality : 0.043 0.126 502 Planarity : 0.004 0.041 591 Dihedral : 5.735 57.062 468 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 18.88 % Favored : 79.65 % 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: 1.92 (0.43), residues: 415 helix: 2.63 (0.35), residues: 212 sheet: -0.31 (0.71), residues: 62 loop : -0.06 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 263 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.008 0.001 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.51 seconds wall clock time: 33 minutes 59.13 seconds (2039.13 seconds total)