Starting phenix.real_space_refine on Mon Jun 24 16:17:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/06_2024/8xct_38254_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/06_2024/8xct_38254.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/8xct_38254/06_2024/8xct_38254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/06_2024/8xct_38254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/06_2024/8xct_38254_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/06_2024/8xct_38254_neut_updated.pdb" } 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 2120 2.51 5 N 566 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3358 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3330 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 76 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 28} Link IDs: {None: 28} Time building chain proxies: 4.27, per 1000 atoms: 1.27 Number of scatterers: 3358 At special positions: 0 Unit cell: (68.432, 74.448, 73.696, 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 655 8.00 N 566 7.00 C 2120 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: 1.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 48.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.701A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.524A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.653A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.225A 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 removed outlier: 3.503A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 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: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS A 75 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.435A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.209A 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: 7.090A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 161 hydrogen bonds defined for protein. 470 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: 0.89 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1073 1.34 - 1.46: 560 1.46 - 1.57: 1747 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3410 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.093 1.29e-02 6.01e+03 5.19e+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 5.10e+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 4.84e+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=" C6A NDP A 500 " pdb=" N1A NDP A 500 " ideal model delta sigma weight residual 1.368 1.251 0.117 2.90e-02 1.19e+03 1.62e+01 ... (remaining 3405 not shown) Histogram of bond angle deviations from ideal: 96.04 - 103.65: 58 103.65 - 111.26: 1418 111.26 - 118.86: 1358 118.86 - 126.47: 1719 126.47 - 134.07: 82 Bond angle restraints: 4635 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 105.41 127.48 -22.07 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.21 -15.37 1.91e+00 2.73e-01 6.45e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.38 -14.64 1.95e+00 2.62e-01 5.61e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.48 7.98 1.17e+00 7.36e-01 4.68e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.94 8.39 1.48e+00 4.57e-01 3.22e+01 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 1872 23.85 - 47.69: 118 47.69 - 71.54: 24 71.54 - 95.38: 4 95.38 - 119.23: 1 Dihedral angle restraints: 2019 sinusoidal: 823 harmonic: 1196 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 55.81 119.23 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU A 366 " pdb=" CB GLU A 366 " pdb=" CG GLU A 366 " pdb=" CD GLU A 366 " ideal model delta sinusoidal sigma weight residual -180.00 -121.79 -58.21 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 441 0.079 - 0.158: 53 0.158 - 0.237: 3 0.237 - 0.316: 3 0.316 - 0.395: 3 Chirality restraints: 503 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 -0.40 2.00e-01 2.50e+01 3.90e+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 3.26e+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 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 500 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 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=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 862 2.80 - 3.33: 3213 3.33 - 3.85: 5757 3.85 - 4.38: 6998 4.38 - 4.90: 11744 Nonbonded interactions: 28574 Sorted by model distance: nonbonded pdb=" OE2 GLU A 114 " pdb=" O HOH A 601 " model vdw 2.278 2.440 nonbonded pdb=" NE ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.476 2.520 nonbonded pdb=" O VAL A 348 " pdb=" OG SER A 351 " model vdw 2.493 2.440 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.517 2.440 nonbonded pdb=" OE1 GLN A 357 " pdb=" O HOH A 602 " model vdw 2.518 2.440 ... (remaining 28569 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: 0.690 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: 3.390 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 3410 Z= 0.633 Angle : 1.090 22.067 4635 Z= 0.555 Chirality : 0.058 0.395 503 Planarity : 0.011 0.198 589 Dihedral : 16.215 119.230 1257 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.00 % Allowed : 0.88 % Favored : 94.12 % 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: 1.25 (0.42), residues: 416 helix: 2.05 (0.35), residues: 211 sheet: -0.28 (0.69), residues: 66 loop : -0.46 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.353 Fit side-chains REVERT: A 244 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 308 ASN cc_start: 0.7814 (m-40) cc_final: 0.7589 (m-40) outliers start: 17 outliers final: 3 residues processed: 80 average time/residue: 1.4410 time to fit residues: 118.0638 Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 370 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3410 Z= 0.191 Angle : 0.482 4.590 4635 Z= 0.251 Chirality : 0.042 0.156 503 Planarity : 0.005 0.071 589 Dihedral : 8.284 124.434 477 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 1.76 % Allowed : 10.88 % Favored : 87.35 % 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: 1.56 (0.43), residues: 416 helix: 2.29 (0.35), residues: 210 sheet: 0.06 (0.69), residues: 67 loop : -0.40 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.343 Fit side-chains REVERT: A 277 THR cc_start: 0.8230 (m) cc_final: 0.7920 (p) REVERT: A 303 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8042 (pt0) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 1.2437 time to fit residues: 93.4002 Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS 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: 2.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3410 Z= 0.223 Angle : 0.504 9.159 4635 Z= 0.258 Chirality : 0.043 0.154 503 Planarity : 0.005 0.061 589 Dihedral : 7.706 118.736 468 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 12.06 % Favored : 85.29 % 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: 1.47 (0.43), residues: 416 helix: 2.26 (0.35), residues: 210 sheet: -0.23 (0.76), residues: 57 loop : -0.37 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.399 Fit side-chains REVERT: A 277 THR cc_start: 0.8308 (m) cc_final: 0.7923 (p) REVERT: A 303 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8017 (pt0) outliers start: 9 outliers final: 2 residues processed: 68 average time/residue: 1.2772 time to fit residues: 89.2768 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3410 Z= 0.191 Angle : 0.488 11.156 4635 Z= 0.248 Chirality : 0.042 0.139 503 Planarity : 0.005 0.054 589 Dihedral : 7.404 111.260 468 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 12.65 % Favored : 84.41 % 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: 1.44 (0.43), residues: 416 helix: 2.23 (0.35), residues: 210 sheet: -0.22 (0.76), residues: 57 loop : -0.38 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.404 Fit side-chains REVERT: A 204 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8346 (ttpp) REVERT: A 277 THR cc_start: 0.8308 (m) cc_final: 0.7907 (p) REVERT: A 303 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: A 366 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7299 (mt-10) outliers start: 10 outliers final: 3 residues processed: 69 average time/residue: 1.2687 time to fit residues: 90.0843 Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3410 Z= 0.323 Angle : 0.540 12.308 4635 Z= 0.276 Chirality : 0.045 0.163 503 Planarity : 0.005 0.052 589 Dihedral : 7.276 94.024 468 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 3.24 % Allowed : 12.35 % Favored : 84.41 % 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: 1.24 (0.42), residues: 416 helix: 2.01 (0.35), residues: 210 sheet: -0.29 (0.75), residues: 57 loop : -0.40 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.356 Fit side-chains REVERT: A 204 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8342 (ttpp) REVERT: A 277 THR cc_start: 0.8323 (m) cc_final: 0.7882 (p) REVERT: A 286 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 303 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8082 (pt0) outliers start: 11 outliers final: 2 residues processed: 65 average time/residue: 1.3358 time to fit residues: 89.1872 Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8522 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3410 Z= 0.161 Angle : 0.494 11.734 4635 Z= 0.247 Chirality : 0.042 0.123 503 Planarity : 0.005 0.047 589 Dihedral : 6.456 74.192 468 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.35 % Allowed : 13.82 % Favored : 83.82 % 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: 1.33 (0.43), residues: 416 helix: 2.13 (0.35), residues: 210 sheet: -0.20 (0.76), residues: 57 loop : -0.45 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.414 Fit side-chains REVERT: A 13 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: A 277 THR cc_start: 0.8297 (m) cc_final: 0.7885 (p) REVERT: A 298 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: A 303 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: A 366 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7245 (mt-10) outliers start: 8 outliers final: 0 residues processed: 68 average time/residue: 1.2632 time to fit residues: 88.3138 Evaluate side-chains 69 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8543 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3410 Z= 0.210 Angle : 0.481 8.907 4635 Z= 0.246 Chirality : 0.043 0.135 503 Planarity : 0.005 0.046 589 Dihedral : 5.978 61.320 468 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.65 % Allowed : 13.53 % Favored : 83.82 % 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: 1.37 (0.43), residues: 416 helix: 2.12 (0.35), residues: 210 sheet: -0.22 (0.76), residues: 57 loop : -0.34 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.364 Fit side-chains REVERT: A 13 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: A 277 THR cc_start: 0.8316 (m) cc_final: 0.7909 (p) REVERT: A 298 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: A 303 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8093 (pt0) outliers start: 9 outliers final: 0 residues processed: 65 average time/residue: 1.2980 time to fit residues: 86.7522 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 28 optimal weight: 5.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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: 0.8521 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3410 Z= 0.179 Angle : 0.476 8.941 4635 Z= 0.243 Chirality : 0.042 0.125 503 Planarity : 0.004 0.046 589 Dihedral : 4.939 47.900 465 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 15.00 % Favored : 83.53 % 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: 1.42 (0.43), residues: 416 helix: 2.16 (0.35), residues: 211 sheet: -0.16 (0.76), residues: 57 loop : -0.36 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.410 Fit side-chains REVERT: A 13 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: A 246 ARG cc_start: 0.5529 (mpt180) cc_final: 0.5280 (mpt180) REVERT: A 250 TYR cc_start: 0.8207 (t80) cc_final: 0.7976 (t80) REVERT: A 277 THR cc_start: 0.8341 (m) cc_final: 0.7950 (p) REVERT: A 298 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: A 303 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8094 (pt0) outliers start: 5 outliers final: 0 residues processed: 65 average time/residue: 1.2315 time to fit residues: 82.4742 Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 303 GLU 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: 6.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3410 Z= 0.186 Angle : 0.477 8.875 4635 Z= 0.243 Chirality : 0.042 0.126 503 Planarity : 0.004 0.046 589 Dihedral : 4.708 44.841 465 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.76 % Allowed : 14.41 % Favored : 83.82 % 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: 1.48 (0.43), residues: 416 helix: 2.22 (0.35), residues: 210 sheet: -0.48 (0.81), residues: 52 loop : -0.17 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.363 Fit side-chains REVERT: A 13 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: A 277 THR cc_start: 0.8351 (m) cc_final: 0.7967 (p) REVERT: A 303 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8093 (pt0) outliers start: 6 outliers final: 1 residues processed: 67 average time/residue: 1.1930 time to fit residues: 82.3399 Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3410 Z= 0.170 Angle : 0.480 9.133 4635 Z= 0.243 Chirality : 0.042 0.125 503 Planarity : 0.004 0.046 589 Dihedral : 4.589 43.025 465 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.18 % Allowed : 15.00 % Favored : 83.82 % 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: 1.50 (0.43), residues: 416 helix: 2.25 (0.35), residues: 211 sheet: -0.48 (0.81), residues: 52 loop : -0.19 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.296 Fit side-chains REVERT: A 13 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6986 (mt0) REVERT: A 277 THR cc_start: 0.8326 (m) cc_final: 0.7995 (p) REVERT: A 303 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8085 (pt0) outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 1.2135 time to fit residues: 84.8879 Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.089652 restraints weight = 6426.791| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.00 r_work: 0.2606 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 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 = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3410 Z= 0.290 Angle : 0.519 8.802 4635 Z= 0.267 Chirality : 0.044 0.145 503 Planarity : 0.005 0.046 589 Dihedral : 4.850 44.314 465 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.14 % Rotamer: Outliers : 1.76 % Allowed : 15.29 % Favored : 82.94 % 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: 1.37 (0.43), residues: 416 helix: 2.13 (0.35), residues: 210 sheet: -0.22 (0.76), residues: 57 loop : -0.35 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.006 0.001 HIS A 388 PHE 0.013 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2018.28 seconds wall clock time: 36 minutes 23.48 seconds (2183.48 seconds total)