Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:23:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyy_30019/04_2023/6lyy_30019_updated.pdb" } resolution = 3.2 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= 0.007 sd= 0.120 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 S 26 5.16 5 C 2670 2.51 5 N 694 2.21 5 O 711 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "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: 4104 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2902 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1167 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 277 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EY0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.82, per 1000 atoms: 0.69 Number of scatterers: 4104 At special positions: 0 Unit cell: (104.736, 62.187, 120.01, 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 26 16.00 F 3 9.00 O 711 8.00 N 694 7.00 C 2670 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: 1.97 Conformation dependent library (CDL) restraints added in 696.6 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 4 sheets defined 60.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 17 through 34 removed outlier: 4.495A pdb=" N ILE A 24 " --> pdb=" O TRP A 20 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.848A pdb=" N VAL A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 Processing helix chain 'A' and resid 56 through 82 removed outlier: 4.844A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 86 through 105 removed outlier: 4.421A pdb=" N PHE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 138 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 143 through 171 removed outlier: 5.000A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.301A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 4.028A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 261 through 275 removed outlier: 4.315A pdb=" N GLY A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 295 through 321 removed outlier: 4.339A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 330 through 346 removed outlier: 4.756A pdb=" N ALA A 335 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 382 removed outlier: 4.608A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.985A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 Proline residue: A 406 - end of helix removed outlier: 3.807A pdb=" N LEU A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.943A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 4.267A pdb=" N LEU A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 206 through 237 Proline residue: B 211 - end of helix Proline residue: B 235 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 25 through 32 Processing sheet with id= B, first strand: chain 'B' and resid 95 through 101 removed outlier: 4.066A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 113 through 115 removed outlier: 8.600A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 765 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: 1.31 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 643 1.31 - 1.43: 1151 1.43 - 1.56: 2349 1.56 - 1.68: 13 1.68 - 1.81: 40 Bond restraints: 4196 Sorted by residual: bond pdb=" C30 EY0 A 601 " pdb=" C31 EY0 A 601 " ideal model delta sigma weight residual 1.532 1.323 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C30 EY0 A 601 " pdb=" O29 EY0 A 601 " ideal model delta sigma weight residual 1.418 1.610 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C4 EY0 A 601 " pdb=" O10 EY0 A 601 " ideal model delta sigma weight residual 1.218 1.407 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C27 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.334 1.481 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C32 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.450 1.557 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 4191 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.02: 106 106.02 - 113.06: 2133 113.06 - 120.11: 1679 120.11 - 127.15: 1772 127.15 - 134.20: 46 Bond angle restraints: 5736 Sorted by residual: angle pdb=" OG1 THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 109.30 119.64 -10.34 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.98 -6.86 1.34e+00 5.57e-01 2.62e+01 angle pdb=" C THR B 28 " pdb=" CA THR B 28 " pdb=" CB THR B 28 " ideal model delta sigma weight residual 109.51 117.99 -8.48 1.71e+00 3.42e-01 2.46e+01 angle pdb=" CA THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 110.50 118.78 -8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" C GLY B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta sigma weight residual 122.47 126.79 -4.32 8.90e-01 1.26e+00 2.36e+01 ... (remaining 5731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 2113 14.71 - 29.42: 189 29.42 - 44.13: 56 44.13 - 58.84: 10 58.84 - 73.55: 5 Dihedral angle restraints: 2373 sinusoidal: 692 harmonic: 1681 Sorted by residual: dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.08 17.08 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.14 -15.74 0 2.50e+00 1.60e-01 3.97e+01 dihedral pdb=" C VAL B 61 " pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta harmonic sigma weight residual -122.00 -136.20 14.20 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 2370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 655 0.260 - 0.520: 14 0.520 - 0.781: 2 0.781 - 1.041: 0 1.041 - 1.301: 1 Chirality restraints: 672 Sorted by residual: chirality pdb=" CB THR A 108 " pdb=" CA THR A 108 " pdb=" OG1 THR A 108 " pdb=" CG2 THR A 108 " both_signs ideal model delta sigma weight residual False 2.55 1.25 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 669 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY B 103 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 104 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 55 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C TRP B 55 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP B 55 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 323 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 324 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.029 5.00e-02 4.00e+02 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 124 2.70 - 3.25: 4425 3.25 - 3.80: 6281 3.80 - 4.35: 7558 4.35 - 4.90: 12320 Nonbonded interactions: 30708 Sorted by model distance: nonbonded pdb=" O THR A 351 " pdb=" OG1 THR A 352 " model vdw 2.152 2.440 nonbonded pdb=" ND1 HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 2.217 3.200 nonbonded pdb=" CD2 LEU A 281 " pdb=" F24 EY0 A 601 " model vdw 2.269 3.410 nonbonded pdb=" O GLY A 173 " pdb=" OG SER A 177 " model vdw 2.333 2.440 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 2.335 2.440 ... (remaining 30703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.030 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 16.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 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 : 0.010 0.209 4196 Z= 0.726 Angle : 1.163 10.338 5736 Z= 0.739 Chirality : 0.100 1.301 672 Planarity : 0.005 0.052 727 Dihedral : 13.410 73.546 1305 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.90 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 7.41 % 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: -3.75 (0.30), residues: 591 helix: -2.37 (0.23), residues: 348 sheet: -0.47 (0.50), residues: 104 loop : -3.81 (0.39), residues: 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.386 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 72 average time/residue: 0.1831 time to fit residues: 16.3190 Evaluate side-chains 52 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 340 ASN B 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4196 Z= 0.248 Angle : 0.706 6.183 5736 Z= 0.363 Chirality : 0.044 0.162 672 Planarity : 0.004 0.037 727 Dihedral : 5.073 41.151 635 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.70 (0.34), residues: 591 helix: -0.81 (0.27), residues: 353 sheet: 0.28 (0.51), residues: 110 loop : -2.89 (0.50), residues: 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.429 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.1349 time to fit residues: 14.5996 Evaluate side-chains 75 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0472 time to fit residues: 1.1037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 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 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4196 Z= 0.214 Angle : 0.625 7.182 5736 Z= 0.322 Chirality : 0.043 0.145 672 Planarity : 0.004 0.041 727 Dihedral : 4.656 33.679 635 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.36), residues: 591 helix: -0.15 (0.29), residues: 352 sheet: 0.74 (0.52), residues: 104 loop : -2.57 (0.51), residues: 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.411 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 89 average time/residue: 0.1134 time to fit residues: 13.9555 Evaluate side-chains 77 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0623 time to fit residues: 1.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 25 optimal weight: 0.0370 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5161 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 4196 Z= 0.168 Angle : 0.599 7.874 5736 Z= 0.301 Chirality : 0.042 0.138 672 Planarity : 0.004 0.037 727 Dihedral : 4.416 27.151 635 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 591 helix: 0.19 (0.29), residues: 352 sheet: 0.93 (0.52), residues: 104 loop : -2.13 (0.55), residues: 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.441 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 81 average time/residue: 0.1149 time to fit residues: 12.7721 Evaluate side-chains 72 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0473 time to fit residues: 0.9160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5228 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4196 Z= 0.184 Angle : 0.592 7.599 5736 Z= 0.295 Chirality : 0.042 0.141 672 Planarity : 0.004 0.043 727 Dihedral : 4.320 23.618 635 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.37), residues: 591 helix: 0.33 (0.29), residues: 352 sheet: 1.01 (0.51), residues: 104 loop : -1.97 (0.57), residues: 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.456 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1139 time to fit residues: 14.0871 Evaluate side-chains 84 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0538 time to fit residues: 1.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.0370 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5198 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 4196 Z= 0.162 Angle : 0.591 8.879 5736 Z= 0.292 Chirality : 0.041 0.129 672 Planarity : 0.004 0.042 727 Dihedral : 4.278 27.007 635 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.37), residues: 591 helix: 0.53 (0.29), residues: 352 sheet: 1.21 (0.52), residues: 104 loop : -1.94 (0.57), residues: 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.443 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.1360 time to fit residues: 14.8826 Evaluate side-chains 79 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0451 time to fit residues: 0.8811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.5262 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4196 Z= 0.181 Angle : 0.586 7.087 5736 Z= 0.295 Chirality : 0.041 0.136 672 Planarity : 0.004 0.045 727 Dihedral : 4.216 21.322 635 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.37), residues: 591 helix: 0.65 (0.29), residues: 352 sheet: 1.39 (0.53), residues: 102 loop : -1.90 (0.57), residues: 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.456 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.1240 time to fit residues: 15.0882 Evaluate side-chains 84 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0561 time to fit residues: 1.0521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.0040 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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: 0.5277 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4196 Z= 0.182 Angle : 0.589 7.124 5736 Z= 0.297 Chirality : 0.042 0.131 672 Planarity : 0.004 0.049 727 Dihedral : 4.209 21.303 635 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.37), residues: 591 helix: 0.74 (0.29), residues: 348 sheet: 1.45 (0.53), residues: 102 loop : -1.90 (0.56), residues: 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.461 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 0.1197 time to fit residues: 14.0514 Evaluate side-chains 85 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0465 time to fit residues: 1.0024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5301 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4196 Z= 0.186 Angle : 0.582 7.213 5736 Z= 0.297 Chirality : 0.042 0.133 672 Planarity : 0.004 0.052 727 Dihedral : 4.230 21.812 635 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.37), residues: 591 helix: 0.70 (0.29), residues: 355 sheet: 1.69 (0.55), residues: 100 loop : -1.85 (0.56), residues: 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.436 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.1053 time to fit residues: 12.7699 Evaluate side-chains 87 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0468 time to fit residues: 0.9365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 4196 Z= 0.313 Angle : 0.699 6.989 5736 Z= 0.365 Chirality : 0.046 0.177 672 Planarity : 0.005 0.068 727 Dihedral : 4.823 23.512 635 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.36), residues: 591 helix: 0.14 (0.28), residues: 358 sheet: 1.02 (0.54), residues: 107 loop : -1.95 (0.57), residues: 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.468 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.0922 time to fit residues: 12.9603 Evaluate side-chains 94 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0683 time to fit residues: 0.9457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 30.0000 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 53 optimal weight: 20.0000 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 30.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN B 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.229119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.197738 restraints weight = 6413.818| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.84 r_work: 0.4180 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4196 Z= 0.186 Angle : 0.633 9.173 5736 Z= 0.322 Chirality : 0.042 0.124 672 Planarity : 0.004 0.058 727 Dihedral : 4.488 21.569 635 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.37), residues: 591 helix: 0.57 (0.29), residues: 354 sheet: 1.13 (0.54), residues: 108 loop : -1.70 (0.60), residues: 129 =============================================================================== Job complete usr+sys time: 1178.14 seconds wall clock time: 21 minutes 41.38 seconds (1301.38 seconds total)