Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:27:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckr_30391/04_2023/7ckr_30391_updated.pdb" } resolution = 3.0 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= 0.004 sd= 0.070 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 Cl 1 4.86 5 C 2669 2.51 5 N 687 2.21 5 O 711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4094 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2900 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1166 Classifications: {'peptide': 215} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 155} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 204} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 438 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': 7} Unresolved non-hydrogen planarities: 282 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G5O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.34, per 1000 atoms: 0.82 Number of scatterers: 4094 At special positions: 0 Unit cell: (102.883, 58.1877, 112.159, 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) Cl 1 17.00 S 26 16.00 O 711 8.00 N 687 7.00 C 2669 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: 1.91 Conformation dependent library (CDL) restraints added in 603.6 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: 1066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 4 sheets defined 61.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 18 through 51 Proline residue: A 37 - end of helix removed outlier: 3.643A pdb=" N PHE A 44 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 46 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.983A pdb=" N TRP A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 86 through 105 Processing helix chain 'A' and resid 109 through 138 Proline residue: A 130 - end of helix removed outlier: 3.634A pdb=" N THR A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 Proline residue: A 155 - end of helix removed outlier: 3.802A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.949A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 261 through 277 removed outlier: 4.048A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (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 290 Processing helix chain 'A' and resid 295 through 320 removed outlier: 3.576A pdb=" N ALA A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 349 Proline residue: A 327 - end of helix removed outlier: 5.364A pdb=" N GLN A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 353 through 381 removed outlier: 3.918A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 415 Proline residue: A 401 - end of helix removed outlier: 4.226A pdb=" N LEU A 404 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 420 through 448 removed outlier: 3.820A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (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 209 through 236 Proline residue: B 235 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 25 through 33 Processing sheet with id= B, first strand: chain 'B' and resid 95 through 100 removed outlier: 4.067A 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 117 removed outlier: 8.602A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE B 116 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 201 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.419A 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) 301 hydrogen bonds defined for protein. 804 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: 1.21 Time building geometry restraints manager: 1.99 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: 644 1.31 - 1.43: 1150 1.43 - 1.56: 2344 1.56 - 1.69: 8 1.69 - 1.81: 41 Bond restraints: 4187 Sorted by residual: bond pdb=" C12 G5O A 601 " pdb=" C13 G5O A 601 " ideal model delta sigma weight residual 1.387 1.525 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C10 G5O A 601 " pdb=" C11 G5O A 601 " ideal model delta sigma weight residual 1.388 1.524 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C14 G5O A 601 " pdb=" C15 G5O A 601 " ideal model delta sigma weight residual 1.387 1.522 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C17 G5O A 601 " pdb=" N18 G5O A 601 " ideal model delta sigma weight residual 1.339 1.453 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 1.474 1.538 -0.064 1.40e-02 5.10e+03 2.10e+01 ... (remaining 4182 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.25: 80 105.25 - 112.51: 2058 112.51 - 119.76: 1461 119.76 - 127.02: 2077 127.02 - 134.27: 44 Bond angle restraints: 5720 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.99 13.51 1.40e+00 5.10e-01 9.31e+01 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 111.50 98.07 13.43 1.40e+00 5.10e-01 9.21e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.09 12.41 1.40e+00 5.10e-01 7.85e+01 angle pdb=" O8 G5O A 601 " pdb=" S7 G5O A 601 " pdb=" O9 G5O A 601 " ideal model delta sigma weight residual 119.81 101.59 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.96 -6.84 1.34e+00 5.57e-01 2.61e+01 ... (remaining 5715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2056 16.50 - 33.01: 200 33.01 - 49.51: 82 49.51 - 66.02: 27 66.02 - 82.52: 4 Dihedral angle restraints: 2369 sinusoidal: 690 harmonic: 1679 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 -139.04 17.04 0 2.50e+00 1.60e-01 4.65e+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 123.40 139.11 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA TYR A 293 " pdb=" C TYR A 293 " pdb=" N SER A 294 " pdb=" CA SER A 294 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 2366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 595 0.112 - 0.224: 60 0.224 - 0.336: 7 0.336 - 0.448: 5 0.448 - 0.560: 3 Chirality restraints: 670 Sorted by residual: 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 7.84e+00 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 7.74e+00 chirality pdb=" CA GLU B 155 " pdb=" N GLU B 155 " pdb=" C GLU B 155 " pdb=" CB GLU B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 131 " 0.117 5.00e-02 4.00e+02 1.63e-01 4.28e+01 pdb=" N PRO B 132 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 90 " -0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO B 91 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 27 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C PHE A 27 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 27 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 28 " -0.015 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 24 2.50 - 3.10: 3323 3.10 - 3.70: 6200 3.70 - 4.30: 8836 4.30 - 4.90: 14450 Nonbonded interactions: 32833 Sorted by model distance: nonbonded pdb=" O GLY A 173 " pdb=" OG SER A 177 " model vdw 1.896 2.440 nonbonded pdb=" O PRO A 324 " pdb=" NH1 ARG A 328 " model vdw 1.989 2.520 nonbonded pdb=" OE1 GLN A 330 " pdb=" OG1 THR A 377 " model vdw 2.059 2.440 nonbonded pdb=" O LYS A 38 " pdb=" OG1 THR A 41 " model vdw 2.141 2.440 nonbonded pdb=" OD1 ASP A 418 " pdb=" N TYR A 419 " model vdw 2.157 2.520 ... (remaining 32828 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.138 4187 Z= 0.667 Angle : 1.223 18.216 5720 Z= 0.792 Chirality : 0.085 0.560 670 Planarity : 0.010 0.163 731 Dihedral : 17.221 82.520 1303 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer Outliers : 11.04 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 11.11 % 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: -2.89 (0.31), residues: 591 helix: -1.92 (0.24), residues: 357 sheet: 0.30 (0.53), residues: 94 loop : -2.94 (0.43), residues: 140 *********************** 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 108 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 71 time to evaluate : 0.403 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 99 average time/residue: 0.6031 time to fit residues: 63.5342 Evaluate side-chains 79 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0394 time to fit residues: 0.7419 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 330 GLN B 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 4187 Z= 0.240 Angle : 0.691 7.615 5720 Z= 0.361 Chirality : 0.044 0.125 670 Planarity : 0.007 0.063 731 Dihedral : 4.984 30.868 631 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 7.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.68 (0.35), residues: 591 helix: -0.13 (0.28), residues: 362 sheet: 0.89 (0.53), residues: 101 loop : -2.18 (0.51), 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 113 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.442 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.4546 time to fit residues: 53.2835 Evaluate side-chains 91 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.5594 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.0040 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.5932 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4187 Z= 0.204 Angle : 0.651 7.883 5720 Z= 0.335 Chirality : 0.044 0.180 670 Planarity : 0.006 0.048 731 Dihedral : 4.654 32.094 631 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 6.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.05 (0.36), residues: 591 helix: 0.49 (0.30), residues: 352 sheet: 1.06 (0.52), residues: 101 loop : -1.76 (0.49), residues: 138 *********************** 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 103 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.493 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 0.4215 time to fit residues: 45.2370 Evaluate side-chains 91 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1313 time to fit residues: 0.9377 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 0.0470 chunk 47 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4187 Z= 0.217 Angle : 0.655 8.450 5720 Z= 0.338 Chirality : 0.044 0.160 670 Planarity : 0.006 0.052 731 Dihedral : 4.673 30.552 631 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 6.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.11 (0.36), residues: 591 helix: 0.38 (0.29), residues: 359 sheet: 1.28 (0.51), residues: 101 loop : -1.55 (0.53), residues: 131 *********************** 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 114 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.436 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 111 average time/residue: 0.4562 time to fit residues: 54.9768 Evaluate side-chains 97 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.0823 time to fit residues: 0.7111 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4187 Z= 0.216 Angle : 0.672 7.768 5720 Z= 0.348 Chirality : 0.046 0.218 670 Planarity : 0.006 0.054 731 Dihedral : 4.592 30.761 631 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 5.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.25 (0.36), residues: 591 helix: 0.47 (0.29), residues: 359 sheet: 1.34 (0.51), residues: 101 loop : -1.41 (0.54), residues: 131 *********************** 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 108 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.475 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.4663 time to fit residues: 52.5364 Evaluate side-chains 97 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0822 time to fit residues: 0.7333 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4187 Z= 0.178 Angle : 0.643 9.404 5720 Z= 0.329 Chirality : 0.044 0.207 670 Planarity : 0.006 0.059 731 Dihedral : 4.326 30.591 631 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 5.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.57 (0.37), residues: 591 helix: 0.76 (0.30), residues: 349 sheet: 1.46 (0.51), residues: 101 loop : -1.26 (0.52), residues: 141 *********************** 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 109 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.431 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.5644 time to fit residues: 62.3211 Evaluate side-chains 98 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.0926 time to fit residues: 0.9025 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4187 Z= 0.207 Angle : 0.656 8.498 5720 Z= 0.343 Chirality : 0.046 0.185 670 Planarity : 0.006 0.053 731 Dihedral : 4.414 30.252 631 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 6.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.54 (0.36), residues: 591 helix: 0.66 (0.30), residues: 354 sheet: 1.58 (0.50), residues: 101 loop : -1.25 (0.54), residues: 136 *********************** 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 112 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.445 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.4993 time to fit residues: 56.5394 Evaluate side-chains 99 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.7955 time to fit residues: 2.2718 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 4187 Z= 0.384 Angle : 0.806 10.050 5720 Z= 0.430 Chirality : 0.052 0.251 670 Planarity : 0.007 0.060 731 Dihedral : 5.484 31.916 631 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 7.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.03 (0.35), residues: 591 helix: 0.24 (0.28), residues: 350 sheet: 1.41 (0.48), residues: 111 loop : -1.60 (0.56), residues: 130 *********************** 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 122 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.469 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 115 average time/residue: 0.4891 time to fit residues: 60.8327 Evaluate side-chains 102 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0887 time to fit residues: 0.8516 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 4187 Z= 0.246 Angle : 0.730 9.806 5720 Z= 0.384 Chirality : 0.048 0.255 670 Planarity : 0.006 0.053 731 Dihedral : 5.004 31.714 631 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.24 (0.36), residues: 591 helix: 0.39 (0.29), residues: 355 sheet: 1.43 (0.49), residues: 111 loop : -1.47 (0.58), residues: 125 *********************** 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 109 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.450 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 107 average time/residue: 0.4584 time to fit residues: 53.2761 Evaluate side-chains 104 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0920 time to fit residues: 0.7607 ------------------------------------------------------------------------------- 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: 9.9990 chunk 46 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4187 Z= 0.212 Angle : 0.715 9.916 5720 Z= 0.369 Chirality : 0.047 0.263 670 Planarity : 0.006 0.059 731 Dihedral : 4.671 32.014 631 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.61 (0.36), residues: 591 helix: 0.78 (0.30), residues: 346 sheet: 1.51 (0.49), residues: 111 loop : -1.41 (0.54), residues: 134 ********************** 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 105 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.454 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 104 average time/residue: 0.4761 time to fit residues: 53.6415 Evaluate side-chains 100 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0849 time to fit residues: 0.7119 ------------------------------------------------------------------------------- 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: 0.0370 chunk 19 optimal weight: 0.0570 chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 40.0000 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.227860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.198452 restraints weight = 5329.721| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.97 r_work: 0.4208 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4187 Z= 0.199 Angle : 0.709 9.481 5720 Z= 0.365 Chirality : 0.047 0.269 670 Planarity : 0.006 0.055 731 Dihedral : 4.528 31.622 631 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.75 (0.36), residues: 591 helix: 0.85 (0.30), residues: 346 sheet: 1.63 (0.49), residues: 111 loop : -1.28 (0.54), residues: 134 =============================================================================== Job complete usr+sys time: 1620.06 seconds wall clock time: 29 minutes 22.89 seconds (1762.89 seconds total)