Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 23:01:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/07_2023/6vu8_21388_updated.pdb" } resolution = 4.14 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 3313 2.51 5 N 913 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 8": "OD1" <-> "OD2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5249 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3815 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 461} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1434 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 3.22, per 1000 atoms: 0.61 Number of scatterers: 5249 At special positions: 0 Unit cell: (118.72, 64.66, 87.98, 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 30 16.00 P 2 15.00 O 991 8.00 N 913 7.00 C 3313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 794.3 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 1 sheets defined 48.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 15 through 28 removed outlier: 4.233A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 56 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 241 through 259 removed outlier: 4.609A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.884A pdb=" N HIS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.781A pdb=" N LYS A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A 350 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.886A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.839A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 removed outlier: 6.388A pdb=" N GLY A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 335 through 350 removed outlier: 4.238A pdb=" N ALA B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 339 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 350 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.036A pdb=" N GLU B 318 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 266 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 320 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 268 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS B 322 " --> pdb=" O LEU B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 192 hydrogen bonds defined for protein. 546 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: 1.17 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1770 1.34 - 1.46: 1040 1.46 - 1.58: 2479 1.58 - 1.70: 7 1.70 - 1.81: 44 Bond restraints: 5340 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.608 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O3P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C ALA A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.337 1.374 -0.036 1.24e-02 6.50e+03 8.64e+00 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.481 0.047 2.00e-02 2.50e+03 5.51e+00 ... (remaining 5335 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.05: 83 105.05 - 112.30: 2604 112.30 - 119.55: 1960 119.55 - 126.80: 2523 126.80 - 134.05: 58 Bond angle restraints: 7228 Sorted by residual: angle pdb=" C GLN A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N SER A 30 " pdb=" CA SER A 30 " pdb=" C SER A 30 " ideal model delta sigma weight residual 110.97 115.96 -4.99 1.09e+00 8.42e-01 2.09e+01 angle pdb=" C ARG B 313 " pdb=" N LYS B 314 " pdb=" CA LYS B 314 " ideal model delta sigma weight residual 122.61 129.06 -6.45 1.56e+00 4.11e-01 1.71e+01 angle pdb=" C VAL B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 120.82 126.64 -5.82 1.41e+00 5.03e-01 1.70e+01 angle pdb=" CA LEU A 424 " pdb=" CB LEU A 424 " pdb=" CG LEU A 424 " ideal model delta sigma weight residual 116.30 130.15 -13.85 3.50e+00 8.16e-02 1.56e+01 ... (remaining 7223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2835 17.89 - 35.78: 355 35.78 - 53.67: 54 53.67 - 71.55: 11 71.55 - 89.44: 9 Dihedral angle restraints: 3264 sinusoidal: 1306 harmonic: 1958 Sorted by residual: dihedral pdb=" CA ASN A 207 " pdb=" C ASN A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ARG A 365 " pdb=" C ARG A 365 " pdb=" N PRO A 366 " pdb=" CA PRO A 366 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA B 41 " pdb=" C ALA B 41 " pdb=" N GLY B 42 " pdb=" CA GLY B 42 " ideal model delta harmonic sigma weight residual 180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 675 0.067 - 0.134: 137 0.134 - 0.202: 16 0.202 - 0.269: 2 0.269 - 0.336: 1 Chirality restraints: 831 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CG LEU A 418 " pdb=" CB LEU A 418 " pdb=" CD1 LEU A 418 " pdb=" CD2 LEU A 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 377 " pdb=" CA VAL A 377 " pdb=" CG1 VAL A 377 " pdb=" CG2 VAL A 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 828 not shown) Planarity restraints: 939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 365 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO A 366 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 287 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 288 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 204 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.035 5.00e-02 4.00e+02 ... (remaining 936 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1331 2.79 - 3.32: 5068 3.32 - 3.84: 8478 3.84 - 4.37: 9470 4.37 - 4.90: 15265 Nonbonded interactions: 39612 Sorted by model distance: nonbonded pdb=" O PHE A 270 " pdb=" OG1 THR A 274 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU A 197 " pdb=" OH TYR A 249 " model vdw 2.313 2.440 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 260 " model vdw 2.317 2.440 nonbonded pdb=" O PHE A 406 " pdb=" OG1 THR A 410 " model vdw 2.326 2.440 nonbonded pdb=" NH2 ARG A 255 " pdb=" O LEU A 286 " model vdw 2.334 2.520 ... (remaining 39607 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 1.340 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.104 5340 Z= 0.381 Angle : 1.053 13.846 7228 Z= 0.553 Chirality : 0.054 0.336 831 Planarity : 0.007 0.065 939 Dihedral : 16.207 89.443 1986 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.24), residues: 655 helix: -2.78 (0.20), residues: 332 sheet: -3.68 (0.93), residues: 21 loop : -3.80 (0.29), residues: 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1716 time to fit residues: 38.6731 Evaluate side-chains 128 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 40 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 90 HIS A 229 ASN A 344 HIS B 304 GLN B 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5340 Z= 0.183 Angle : 0.655 7.718 7228 Z= 0.340 Chirality : 0.040 0.169 831 Planarity : 0.005 0.053 939 Dihedral : 6.213 25.354 730 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.30), residues: 655 helix: -1.02 (0.27), residues: 330 sheet: -3.50 (0.95), residues: 21 loop : -3.42 (0.31), residues: 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.1308 time to fit residues: 30.5772 Evaluate side-chains 135 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 0.0060 chunk 48 optimal weight: 9.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS A 229 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS B 256 ASN B 304 GLN B 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5340 Z= 0.173 Angle : 0.658 8.287 7228 Z= 0.334 Chirality : 0.041 0.169 831 Planarity : 0.005 0.067 939 Dihedral : 5.688 23.623 730 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.31), residues: 655 helix: -0.33 (0.29), residues: 323 sheet: -3.39 (0.95), residues: 21 loop : -3.26 (0.32), residues: 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1462 time to fit residues: 34.4069 Evaluate side-chains 137 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 324 HIS A 344 HIS B 304 GLN B 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5340 Z= 0.201 Angle : 0.670 8.387 7228 Z= 0.337 Chirality : 0.042 0.286 831 Planarity : 0.005 0.054 939 Dihedral : 5.523 23.774 730 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.33), residues: 655 helix: -0.05 (0.30), residues: 327 sheet: -3.48 (0.92), residues: 21 loop : -3.14 (0.33), residues: 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 165 average time/residue: 0.1350 time to fit residues: 29.9275 Evaluate side-chains 133 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 229 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 433 GLN B 322 HIS ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 5340 Z= 0.356 Angle : 0.796 7.926 7228 Z= 0.401 Chirality : 0.046 0.254 831 Planarity : 0.005 0.049 939 Dihedral : 5.992 23.265 730 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.32), residues: 655 helix: -0.29 (0.28), residues: 328 sheet: -3.57 (0.90), residues: 21 loop : -3.27 (0.34), residues: 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 0.1436 time to fit residues: 29.5345 Evaluate side-chains 129 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0780 time to fit residues: 0.9568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 53 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 229 ASN A 344 HIS B 304 GLN B 322 HIS B 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5340 Z= 0.168 Angle : 0.708 8.959 7228 Z= 0.349 Chirality : 0.042 0.257 831 Planarity : 0.005 0.051 939 Dihedral : 5.381 23.089 730 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.33), residues: 655 helix: 0.02 (0.29), residues: 344 sheet: -3.65 (0.89), residues: 21 loop : -3.10 (0.34), residues: 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.1459 time to fit residues: 34.3706 Evaluate side-chains 135 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0896 time to fit residues: 1.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 244 HIS B 304 GLN B 322 HIS B 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5340 Z= 0.186 Angle : 0.707 8.220 7228 Z= 0.352 Chirality : 0.043 0.242 831 Planarity : 0.005 0.054 939 Dihedral : 5.310 27.958 730 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.33), residues: 655 helix: 0.02 (0.28), residues: 343 sheet: -3.24 (0.97), residues: 21 loop : -2.97 (0.35), residues: 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 0.1301 time to fit residues: 28.3190 Evaluate side-chains 132 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0829 time to fit residues: 0.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 344 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5340 Z= 0.184 Angle : 0.711 10.435 7228 Z= 0.345 Chirality : 0.042 0.261 831 Planarity : 0.005 0.056 939 Dihedral : 5.242 26.837 730 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.33), residues: 655 helix: 0.12 (0.29), residues: 343 sheet: -2.97 (1.03), residues: 21 loop : -2.87 (0.35), residues: 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1370 time to fit residues: 28.8060 Evaluate side-chains 126 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 123 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5340 Z= 0.291 Angle : 0.791 10.797 7228 Z= 0.392 Chirality : 0.045 0.284 831 Planarity : 0.006 0.081 939 Dihedral : 5.608 29.435 730 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.33), residues: 655 helix: 0.25 (0.29), residues: 330 sheet: -2.41 (1.29), residues: 16 loop : -2.87 (0.35), residues: 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1359 time to fit residues: 28.4016 Evaluate side-chains 124 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.0010 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5340 Z= 0.175 Angle : 0.728 9.319 7228 Z= 0.353 Chirality : 0.042 0.248 831 Planarity : 0.005 0.064 939 Dihedral : 5.300 27.155 730 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.33), residues: 655 helix: 0.24 (0.29), residues: 344 sheet: -2.27 (1.30), residues: 16 loop : -2.96 (0.34), residues: 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1257 time to fit residues: 27.2200 Evaluate side-chains 125 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 0.0000 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 229 ASN A 344 HIS A 414 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.132769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105183 restraints weight = 12542.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108174 restraints weight = 8352.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110296 restraints weight = 6242.276| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5340 Z= 0.174 Angle : 0.729 11.435 7228 Z= 0.350 Chirality : 0.043 0.207 831 Planarity : 0.005 0.058 939 Dihedral : 5.120 26.841 730 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.33), residues: 655 helix: 0.20 (0.29), residues: 344 sheet: -2.10 (1.34), residues: 16 loop : -2.88 (0.34), residues: 295 =============================================================================== Job complete usr+sys time: 1483.44 seconds wall clock time: 27 minutes 18.57 seconds (1638.57 seconds total)