Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:50:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/11_2022/7wsn_32761_updated.pdb" } resolution = 3.31 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= 0.002 sd= 0.116 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3504 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'5RH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.73 Number of scatterers: 3567 At special positions: 0 Unit cell: (92.0125, 58.455, 72.5275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 621 8.00 N 579 7.00 C 2353 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 57 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 581.4 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 Processing helix chain 'A' and resid 48 through 62 removed outlier: 4.339A pdb=" N GLU A 53 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.705A pdb=" N VAL A 85 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 129 through 132 No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 136 through 163 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 167 through 191 removed outlier: 4.137A pdb=" N GLY A 170 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 172 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 Proline residue: A 212 - end of helix removed outlier: 3.631A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 303 through 317 removed outlier: 6.833A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 4.540A pdb=" N GLU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARG A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 372 Processing helix chain 'A' and resid 378 through 397 removed outlier: 4.054A pdb=" N TYR A 382 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 397 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 416 through 445 removed outlier: 5.161A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.504A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 255 hydrogen bonds defined for protein. 630 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: 1.03 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 542 1.31 - 1.43: 967 1.43 - 1.56: 2114 1.56 - 1.68: 1 1.68 - 1.81: 25 Bond restraints: 3649 Sorted by residual: bond pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 1.617 1.320 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C27 5RH A 601 " pdb=" C28 5RH A 601 " ideal model delta sigma weight residual 1.583 1.314 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C2 5RH A 601 " pdb=" C3 5RH A 601 " ideal model delta sigma weight residual 1.697 1.512 0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" C7 5RH A 601 " pdb=" C8 5RH A 601 " ideal model delta sigma weight residual 1.392 1.528 -0.136 2.00e-02 2.50e+03 4.59e+01 bond pdb=" N 5RH A 601 " pdb=" C7 5RH A 601 " ideal model delta sigma weight residual 1.583 1.449 0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 3644 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 93 106.04 - 113.04: 1991 113.04 - 120.04: 1450 120.04 - 127.03: 1396 127.03 - 134.03: 45 Bond angle restraints: 4975 Sorted by residual: angle pdb=" C1 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C3 5RH A 601 " ideal model delta sigma weight residual 69.02 125.28 -56.26 3.00e+00 1.11e-01 3.52e+02 angle pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " pdb=" C20 5RH A 601 " ideal model delta sigma weight residual 85.77 125.80 -40.03 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C1 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C30 5RH A 601 " ideal model delta sigma weight residual 150.15 119.90 30.25 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 154.32 125.50 28.82 3.00e+00 1.11e-01 9.23e+01 angle pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 109.64 113.13 -3.49 5.38e-01 3.45e+00 4.22e+01 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.95: 1865 18.95 - 37.90: 200 37.90 - 56.84: 32 56.84 - 75.79: 11 75.79 - 94.74: 3 Dihedral angle restraints: 2111 sinusoidal: 808 harmonic: 1303 Sorted by residual: dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA VAL A 210 " pdb=" C VAL A 210 " pdb=" N LEU A 211 " pdb=" CA LEU A 211 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O2 5RH A 601 " ideal model delta sinusoidal sigma weight residual 99.85 -165.41 -94.74 1 3.00e+01 1.11e-03 1.15e+01 ... (remaining 2108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 580 0.100 - 0.200: 20 0.200 - 0.300: 1 0.300 - 0.399: 0 0.399 - 0.499: 2 Chirality restraints: 603 Sorted by residual: chirality pdb=" C16 5RH A 601 " pdb=" C15 5RH A 601 " pdb=" C29 5RH A 601 " pdb=" C5 5RH A 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.87 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" C3 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C4 5RH A 601 " pdb=" C5 5RH A 601 " both_signs ideal model delta sigma weight residual False -2.83 -2.41 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C24 5RH A 601 " pdb=" C23 5RH A 601 " pdb=" C25 5RH A 601 " pdb=" C26 5RH A 601 " both_signs ideal model delta sigma weight residual False -2.77 -2.53 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 600 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " 0.062 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 57 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.027 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C18 5RH A 601 " 0.064 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.063 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.066 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C15 5RH A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.021 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.053 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.039 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 872 2.78 - 3.31: 3873 3.31 - 3.84: 5893 3.84 - 4.37: 6677 4.37 - 4.90: 11321 Nonbonded interactions: 28636 Sorted by model distance: nonbonded pdb=" OG SER A 89 " pdb=" ND2 ASN A 431 " model vdw 2.248 2.520 nonbonded pdb=" O GLY A 100 " pdb=" OG SER A 103 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR A 79 " pdb=" OH TYR A 440 " model vdw 2.261 2.440 nonbonded pdb=" O GLY A 92 " pdb=" OG SER A 95 " model vdw 2.372 2.440 nonbonded pdb=" NH2 ARG A 350 " pdb=" O PHE A 465 " model vdw 2.375 2.520 ... (remaining 28631 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2353 2.51 5 N 579 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.330 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: 1.810 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.012 0.297 3649 Z= 0.667 Angle : 1.460 56.260 4975 Z= 0.625 Chirality : 0.053 0.499 603 Planarity : 0.006 0.049 616 Dihedral : 16.294 94.740 1283 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 1.08 % 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: -0.44 (0.39), residues: 461 helix: 0.35 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -2.88 (0.62), residues: 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.365 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1404 time to fit residues: 10.6970 Evaluate side-chains 44 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0422 time to fit residues: 0.6451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 353 HIS A 413 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3649 Z= 0.250 Angle : 0.835 20.114 4975 Z= 0.376 Chirality : 0.044 0.285 603 Planarity : 0.006 0.051 616 Dihedral : 5.974 75.294 513 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.62 % 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: 0.59 (0.40), residues: 461 helix: 1.23 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -2.92 (0.55), residues: 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.433 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.1167 time to fit residues: 8.9715 Evaluate side-chains 52 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0362 time to fit residues: 0.8743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3649 Z= 0.219 Angle : 0.771 20.780 4975 Z= 0.344 Chirality : 0.042 0.244 603 Planarity : 0.006 0.053 616 Dihedral : 5.864 76.991 513 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 1.62 % 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: 1.03 (0.41), residues: 461 helix: 1.52 (0.29), residues: 370 sheet: None (None), residues: 0 loop : -2.92 (0.56), residues: 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.428 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.1206 time to fit residues: 9.2864 Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0614 time to fit residues: 0.9406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 3649 Z= 0.359 Angle : 0.825 20.650 4975 Z= 0.375 Chirality : 0.044 0.233 603 Planarity : 0.006 0.064 616 Dihedral : 6.058 79.059 513 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 2.43 % 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: 0.80 (0.41), residues: 461 helix: 1.35 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -2.91 (0.57), residues: 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.435 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1148 time to fit residues: 7.9775 Evaluate side-chains 53 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0367 time to fit residues: 0.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3649 Z= 0.227 Angle : 0.763 20.820 4975 Z= 0.341 Chirality : 0.041 0.233 603 Planarity : 0.006 0.059 616 Dihedral : 5.824 75.809 513 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.81 % 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: 1.12 (0.41), residues: 461 helix: 1.56 (0.29), residues: 368 sheet: None (None), residues: 0 loop : -2.68 (0.57), residues: 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.412 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1201 time to fit residues: 8.1975 Evaluate side-chains 49 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0377 time to fit residues: 0.7113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3649 Z= 0.201 Angle : 0.758 20.837 4975 Z= 0.333 Chirality : 0.041 0.233 603 Planarity : 0.006 0.054 616 Dihedral : 5.680 73.330 513 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.81 % 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: 1.31 (0.41), residues: 461 helix: 1.70 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.53 (0.57), residues: 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.423 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.1462 time to fit residues: 9.4453 Evaluate side-chains 48 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0374 time to fit residues: 0.6295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3649 Z= 0.231 Angle : 0.759 20.792 4975 Z= 0.335 Chirality : 0.041 0.235 603 Planarity : 0.006 0.057 616 Dihedral : 5.677 73.848 513 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.08 % 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: 1.29 (0.41), residues: 461 helix: 1.67 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.50 (0.56), residues: 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.394 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.1281 time to fit residues: 8.5082 Evaluate side-chains 49 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 21 optimal weight: 0.0020 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3649 Z= 0.178 Angle : 0.726 20.917 4975 Z= 0.320 Chirality : 0.040 0.234 603 Planarity : 0.006 0.053 616 Dihedral : 5.474 70.051 513 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.41), residues: 461 helix: 1.72 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.41 (0.56), residues: 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.396 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 53 average time/residue: 0.1289 time to fit residues: 9.0396 Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 46 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3649 Z= 0.209 Angle : 0.759 20.788 4975 Z= 0.332 Chirality : 0.040 0.236 603 Planarity : 0.006 0.055 616 Dihedral : 5.490 70.883 513 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 1.37 (0.41), residues: 461 helix: 1.72 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.39 (0.56), residues: 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.344 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1235 time to fit residues: 8.7375 Evaluate side-chains 51 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0431 time to fit residues: 0.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.0040 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3649 Z= 0.192 Angle : 0.754 20.830 4975 Z= 0.326 Chirality : 0.040 0.236 603 Planarity : 0.006 0.054 616 Dihedral : 5.437 69.558 513 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.27 % 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: 1.51 (0.41), residues: 461 helix: 1.77 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.37 (0.59), residues: 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.402 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1196 time to fit residues: 8.2160 Evaluate side-chains 47 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115172 restraints weight = 4209.486| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.13 r_work: 0.3305 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3286 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3276 rms_B_bonded: 2.06 restraints_weight: 0.0625 r_work: 0.3266 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3255 rms_B_bonded: 2.26 restraints_weight: 0.0156 r_work: 0.3244 rms_B_bonded: 2.40 restraints_weight: 0.0078 r_work: 0.3232 rms_B_bonded: 2.56 restraints_weight: 0.0039 r_work: 0.3219 rms_B_bonded: 2.74 restraints_weight: 0.0020 r_work: 0.3206 rms_B_bonded: 2.95 restraints_weight: 0.0010 r_work: 0.3192 rms_B_bonded: 3.18 restraints_weight: 0.0005 r_work: 0.3177 rms_B_bonded: 3.44 restraints_weight: 0.0002 r_work: 0.3161 rms_B_bonded: 3.72 restraints_weight: 0.0001 r_work: 0.3144 rms_B_bonded: 4.04 restraints_weight: 0.0001 r_work: 0.3126 rms_B_bonded: 4.39 restraints_weight: 0.0000 r_work: 0.3107 rms_B_bonded: 4.78 restraints_weight: 0.0000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3649 Z= 0.214 Angle : 0.756 20.778 4975 Z= 0.329 Chirality : 0.041 0.236 603 Planarity : 0.006 0.056 616 Dihedral : 5.466 69.888 513 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 1.46 (0.41), residues: 461 helix: 1.73 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -2.36 (0.59), residues: 89 =============================================================================== Job complete usr+sys time: 1071.71 seconds wall clock time: 20 minutes 35.30 seconds (1235.30 seconds total)