Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 06:36:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/04_2023/8gyw_34378_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.102 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 3994 2.51 5 N 984 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6076 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.76, per 1000 atoms: 0.62 Number of scatterers: 6076 At special positions: 0 Unit cell: (97.37, 101.65, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 4 15.00 Mg 4 11.99 O 1042 8.00 N 984 7.00 C 3994 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: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 2 sheets defined 72.9% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 29 through 36 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 78 removed outlier: 4.253A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 Processing helix chain 'B' and resid 116 through 142 removed outlier: 4.374A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 179 through 203 Processing helix chain 'B' and resid 213 through 236 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 246 through 271 Proline residue: B 250 - end of helix removed outlier: 3.942A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 306 removed outlier: 4.229A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 339 Processing helix chain 'B' and resid 349 through 362 removed outlier: 4.030A pdb=" N GLY B 353 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 354 - end of helix removed outlier: 3.539A pdb=" N LEU B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 361 " --> pdb=" O PHE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 399 Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 65 through 78 removed outlier: 4.253A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 Processing helix chain 'A' and resid 116 through 142 removed outlier: 4.374A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.583A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 203 Processing helix chain 'A' and resid 213 through 236 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 246 through 271 Proline residue: A 250 - end of helix removed outlier: 3.942A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.229A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 362 removed outlier: 4.030A pdb=" N GLY A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.539A pdb=" N LEU A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 361 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.790A pdb=" N LEU B 206 " --> pdb=" O ALA B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.791A pdb=" N LEU A 206 " --> pdb=" O ALA A 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 384 hydrogen bonds defined for protein. 1122 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: 1.59 Time building geometry restraints manager: 2.59 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: 1379 1.34 - 1.45: 1411 1.45 - 1.57: 3380 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6248 Sorted by residual: bond pdb=" CB PRO A 115 " pdb=" CG PRO A 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.56e+00 bond pdb=" CB PRO B 115 " pdb=" CG PRO B 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.559 -0.042 1.54e-02 4.22e+03 7.49e+00 bond pdb=" CA PRO B 108 " pdb=" C PRO B 108 " ideal model delta sigma weight residual 1.517 1.558 -0.042 1.54e-02 4.22e+03 7.39e+00 bond pdb=" CB PRO B 108 " pdb=" CG PRO B 108 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.74e+00 ... (remaining 6243 not shown) Histogram of bond angle deviations from ideal: 94.38 - 102.56: 52 102.56 - 110.73: 1929 110.73 - 118.91: 3102 118.91 - 127.08: 3341 127.08 - 135.26: 100 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 112.00 99.70 12.30 1.40e+00 5.10e-01 7.72e+01 angle pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.71e+01 angle pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" CD PRO A 108 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.03e+01 angle pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" CD PRO B 108 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 135.26 -18.96 3.50e+00 8.16e-02 2.93e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3164 16.52 - 33.04: 280 33.04 - 49.56: 98 49.56 - 66.08: 30 66.08 - 82.61: 6 Dihedral angle restraints: 3578 sinusoidal: 1370 harmonic: 2208 Sorted by residual: dihedral pdb=" C PRO B 108 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " pdb=" CB PRO B 108 " ideal model delta harmonic sigma weight residual -120.70 -129.60 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PRO A 108 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " pdb=" CB PRO A 108 " ideal model delta harmonic sigma weight residual -120.70 -129.55 8.85 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " pdb=" OD1 ASP A 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 758 0.081 - 0.162: 188 0.162 - 0.244: 30 0.244 - 0.325: 6 0.325 - 0.406: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR A 214 " pdb=" CA THR A 214 " pdb=" OG1 THR A 214 " pdb=" CG2 THR A 214 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 981 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.103 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO A 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO B 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 107 " -0.094 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO A 108 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.071 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 40 2.59 - 3.17: 5070 3.17 - 3.74: 9924 3.74 - 4.32: 12183 4.32 - 4.90: 20526 Nonbonded interactions: 47743 Sorted by model distance: nonbonded pdb=" OD1 ASP B 154 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP A 154 " pdb="MG MG A 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 502 " pdb=" O2B CDC B 503 " model vdw 2.085 2.170 nonbonded pdb="MG MG A 502 " pdb=" O2B CDC A 503 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb=" OH TYR A 304 " model vdw 2.269 2.440 ... (remaining 47738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 2.250 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.700 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.146 6248 Z= 0.529 Angle : 1.459 18.960 8524 Z= 0.833 Chirality : 0.077 0.406 984 Planarity : 0.015 0.199 1036 Dihedral : 15.176 82.606 2154 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 0.30 % 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 (0.29), residues: 756 helix: 0.99 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 0.67 (0.47), residues: 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1989 time to fit residues: 48.5415 Evaluate side-chains 168 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 197 HIS B 361 GLN A 69 GLN A 197 HIS A 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6248 Z= 0.186 Angle : 0.586 6.659 8524 Z= 0.305 Chirality : 0.041 0.123 984 Planarity : 0.005 0.051 1036 Dihedral : 3.923 19.757 818 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 3.93 % 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: 2.77 (0.29), residues: 756 helix: 2.17 (0.20), residues: 546 sheet: None (None), residues: 0 loop : 1.13 (0.47), residues: 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 186 average time/residue: 0.2176 time to fit residues: 50.8918 Evaluate side-chains 179 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0590 time to fit residues: 2.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.0000 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 6248 Z= 0.244 Angle : 0.593 7.193 8524 Z= 0.307 Chirality : 0.042 0.173 984 Planarity : 0.004 0.032 1036 Dihedral : 3.897 21.893 818 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.46 % Favored : 98.41 % Rotamer Outliers : 3.78 % 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: 2.92 (0.29), residues: 756 helix: 2.29 (0.20), residues: 546 sheet: None (None), residues: 0 loop : 1.14 (0.46), residues: 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.1997 time to fit residues: 47.7327 Evaluate side-chains 175 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0601 time to fit residues: 2.8355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6248 Z= 0.207 Angle : 0.565 8.593 8524 Z= 0.290 Chirality : 0.040 0.153 984 Planarity : 0.004 0.033 1036 Dihedral : 3.851 21.604 818 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 3.17 % 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: 3.00 (0.30), residues: 756 helix: 2.33 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 1.24 (0.48), residues: 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 176 average time/residue: 0.2086 time to fit residues: 46.5559 Evaluate side-chains 165 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0584 time to fit residues: 1.8151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 6248 Z= 0.457 Angle : 0.735 8.567 8524 Z= 0.380 Chirality : 0.046 0.166 984 Planarity : 0.004 0.033 1036 Dihedral : 4.398 25.339 818 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 4.53 % 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: 2.12 (0.30), residues: 756 helix: 1.65 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.95 (0.48), residues: 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 195 average time/residue: 0.2226 time to fit residues: 54.4842 Evaluate side-chains 182 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0660 time to fit residues: 3.2300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6248 Z= 0.188 Angle : 0.586 7.832 8524 Z= 0.301 Chirality : 0.040 0.137 984 Planarity : 0.004 0.032 1036 Dihedral : 4.094 24.656 818 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.30), residues: 756 helix: 1.92 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.18 (0.50), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.667 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 179 average time/residue: 0.1895 time to fit residues: 43.7528 Evaluate side-chains 162 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0595 time to fit residues: 2.0259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 6248 Z= 0.185 Angle : 0.619 8.624 8524 Z= 0.308 Chirality : 0.040 0.135 984 Planarity : 0.004 0.032 1036 Dihedral : 3.927 20.402 818 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.96 % 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: 2.64 (0.31), residues: 756 helix: 2.01 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.22 (0.52), residues: 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.662 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.1810 time to fit residues: 41.6380 Evaluate side-chains 164 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0586 time to fit residues: 2.0458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 197 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 6248 Z= 0.217 Angle : 0.631 10.269 8524 Z= 0.315 Chirality : 0.041 0.161 984 Planarity : 0.004 0.032 1036 Dihedral : 3.942 20.261 818 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.60 % 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: 2.56 (0.30), residues: 756 helix: 1.97 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.11 (0.52), residues: 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 0.697 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 158 average time/residue: 0.1845 time to fit residues: 37.9946 Evaluate side-chains 152 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0553 time to fit residues: 1.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6248 Z= 0.208 Angle : 0.631 9.269 8524 Z= 0.314 Chirality : 0.040 0.132 984 Planarity : 0.004 0.033 1036 Dihedral : 3.891 19.819 818 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.51 % 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: 2.57 (0.30), residues: 756 helix: 1.99 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.08 (0.52), residues: 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.723 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 154 average time/residue: 0.1908 time to fit residues: 38.1807 Evaluate side-chains 153 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0668 time to fit residues: 1.7688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 130 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 6248 Z= 0.205 Angle : 0.636 9.985 8524 Z= 0.318 Chirality : 0.040 0.139 984 Planarity : 0.004 0.032 1036 Dihedral : 3.894 18.881 818 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.60 % 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: 2.60 (0.31), residues: 756 helix: 2.05 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 1.03 (0.50), residues: 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 0.689 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 158 average time/residue: 0.1860 time to fit residues: 38.1949 Evaluate side-chains 155 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0607 time to fit residues: 1.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137470 restraints weight = 8275.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142733 restraints weight = 4445.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146267 restraints weight = 2965.502| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 6248 Z= 0.199 Angle : 0.627 10.479 8524 Z= 0.314 Chirality : 0.040 0.151 984 Planarity : 0.004 0.032 1036 Dihedral : 3.849 18.427 818 Min Nonbonded Distance : 1.170 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.60 % 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: 2.64 (0.31), residues: 756 helix: 2.10 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.98 (0.50), residues: 210 =============================================================================== Job complete usr+sys time: 1490.55 seconds wall clock time: 27 minutes 37.10 seconds (1657.10 seconds total)