Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 14:05:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_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_32761/08_2023/7wsn_32761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/08_2023/7wsn_32761_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 2.23, per 1000 atoms: 0.63 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: 1.70 Conformation dependent library (CDL) restraints added in 695.2 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: 0.67 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: 1.04 Time building geometry restraints manager: 1.83 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=" C27 5RH A 601 " pdb=" C28 5RH A 601 " ideal model delta sigma weight residual 1.572 1.314 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 1.577 1.320 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" N 5RH A 601 " pdb=" C7 5RH A 601 " ideal model delta sigma weight residual 1.666 1.449 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2 5RH A 601 " pdb=" C3 5RH A 601 " ideal model delta sigma weight residual 1.694 1.512 0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C2 5RH A 601 " pdb=" C30 5RH A 601 " ideal model delta sigma weight residual 1.651 1.507 0.144 2.00e-02 2.50e+03 5.21e+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 69.17 125.28 -56.11 3.00e+00 1.11e-01 3.50e+02 angle pdb=" C1 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C30 5RH A 601 " ideal model delta sigma weight residual 149.95 119.90 30.05 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 154.29 125.50 28.79 3.00e+00 1.11e-01 9.21e+01 angle pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " pdb=" C20 5RH A 601 " ideal model delta sigma weight residual 154.29 125.80 28.49 3.00e+00 1.11e-01 9.02e+01 angle pdb=" C3 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C30 5RH A 601 " ideal model delta sigma weight residual 99.68 114.82 -15.14 3.00e+00 1.11e-01 2.55e+01 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 1919 23.09 - 46.17: 159 46.17 - 69.26: 14 69.26 - 92.34: 6 92.34 - 115.43: 1 Dihedral angle restraints: 2099 sinusoidal: 796 harmonic: 1303 Sorted by residual: 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 79.16 -165.41 -115.43 1 3.00e+01 1.11e-03 1.52e+01 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 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 561 0.086 - 0.172: 38 0.172 - 0.258: 2 0.258 - 0.345: 0 0.345 - 0.431: 2 Chirality restraints: 603 Sorted by residual: 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 -2.84 -2.41 -0.43 2.00e-01 2.50e+01 4.64e+00 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 -2.45 -2.87 0.42 2.00e-01 2.50e+01 4.46e+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 -0.25 2.00e-01 2.50e+01 1.51e+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 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: 0.470 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: 1.840 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 0.258 3649 Z= 0.691 Angle : 1.403 56.110 4975 Z= 0.594 Chirality : 0.051 0.431 603 Planarity : 0.006 0.049 616 Dihedral : 16.460 115.430 1271 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 : 0.433 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1426 time to fit residues: 10.7685 Evaluate side-chains 44 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0418 time to fit residues: 0.5714 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7425 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 3649 Z= 0.260 Angle : 0.853 20.193 4975 Z= 0.380 Chirality : 0.044 0.215 603 Planarity : 0.006 0.050 616 Dihedral : 6.363 88.213 501 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.89 % 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: 0.66 (0.41), residues: 461 helix: 1.28 (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 62 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.380 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1128 time to fit residues: 8.8742 Evaluate side-chains 54 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0365 time to fit residues: 0.9448 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7412 moved from start: 0.1709 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= 0.247 Angle : 0.797 21.521 4975 Z= 0.353 Chirality : 0.043 0.219 603 Planarity : 0.006 0.054 616 Dihedral : 5.961 79.595 501 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.35 % 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: 0.99 (0.41), residues: 461 helix: 1.49 (0.29), residues: 370 sheet: None (None), residues: 0 loop : -2.90 (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 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.356 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 0.1235 time to fit residues: 9.2342 Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0383 time to fit residues: 0.6039 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7468 moved from start: 0.1786 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= 0.355 Angle : 0.836 20.998 4975 Z= 0.376 Chirality : 0.044 0.210 603 Planarity : 0.006 0.065 616 Dihedral : 6.038 79.564 501 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.68 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: 0.81 (0.41), residues: 461 helix: 1.35 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -2.92 (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 58 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.411 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1112 time to fit residues: 7.9846 Evaluate side-chains 54 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0410 time to fit residues: 1.1325 ------------------------------------------------------------------------------- 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: 0.2980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.2194 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= 0.194 Angle : 0.751 21.192 4975 Z= 0.333 Chirality : 0.041 0.224 603 Planarity : 0.006 0.055 616 Dihedral : 5.581 73.439 501 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 1.24 (0.41), residues: 461 helix: 1.67 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.66 (0.57), residues: 95 *********************** 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 56 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.393 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.1247 time to fit residues: 9.2782 Evaluate side-chains 52 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0369 time to fit residues: 0.6635 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7382 moved from start: 0.2271 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= 0.225 Angle : 0.754 21.063 4975 Z= 0.335 Chirality : 0.041 0.210 603 Planarity : 0.006 0.055 616 Dihedral : 5.513 73.040 501 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 1.31 (0.41), residues: 461 helix: 1.71 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.56 (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: 4 poor density : 48 time to evaluate : 0.357 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1315 time to fit residues: 8.6089 Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0365 time to fit residues: 0.7200 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2361 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= 0.225 Angle : 0.748 20.982 4975 Z= 0.332 Chirality : 0.041 0.210 603 Planarity : 0.006 0.058 616 Dihedral : 5.392 71.076 501 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.89 % 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 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.53 (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 53 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.396 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1306 time to fit residues: 8.6578 Evaluate side-chains 47 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0372 time to fit residues: 0.7550 ------------------------------------------------------------------------------- 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: 0.3980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3649 Z= 0.211 Angle : 0.738 20.984 4975 Z= 0.328 Chirality : 0.040 0.212 603 Planarity : 0.006 0.057 616 Dihedral : 5.301 69.935 501 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 1.73 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.47 (0.57), 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 51 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.364 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.1126 time to fit residues: 7.6864 Evaluate side-chains 48 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0367 time to fit residues: 0.7528 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 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: 0.7356 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 0.035 3649 Z= 0.205 Angle : 0.735 20.999 4975 Z= 0.327 Chirality : 0.040 0.214 603 Planarity : 0.006 0.056 616 Dihedral : 5.273 69.050 501 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 1.42 (0.41), residues: 461 helix: 1.76 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.42 (0.57), 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 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.389 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1174 time to fit residues: 8.0534 Evaluate side-chains 47 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0379 time to fit residues: 0.6123 ------------------------------------------------------------------------------- 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: 0.1980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3649 Z= 0.176 Angle : 0.722 21.055 4975 Z= 0.318 Chirality : 0.039 0.214 603 Planarity : 0.006 0.052 616 Dihedral : 5.112 67.471 501 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 1.52 (0.41), residues: 461 helix: 1.83 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.38 (0.57), residues: 95 ********************** 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 52 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1323 time to fit residues: 9.1877 Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5599 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- 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 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117854 restraints weight = 4227.651| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.09 r_work: 0.3243 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3649 Z= 0.188 Angle : 0.726 20.971 4975 Z= 0.319 Chirality : 0.040 0.215 603 Planarity : 0.006 0.054 616 Dihedral : 5.067 66.563 501 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.09 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: 1.54 (0.41), residues: 461 helix: 1.78 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -2.32 (0.62), residues: 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1108.16 seconds wall clock time: 20 minutes 42.82 seconds (1242.82 seconds total)