Starting phenix.real_space_refine on Mon Mar 11 08:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytw_34094/03_2024/7ytw_34094_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 5074 2.51 5 N 1238 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3857 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 33, 'TRANS': 473} Chain breaks: 2 Chain: "B" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3857 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 33, 'TRANS': 473} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'ASC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'ASC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.62 Number of scatterers: 7744 At special positions: 0 Unit cell: (87.74, 107.42, 76.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 Na 4 11.00 O 1364 8.00 N 1238 7.00 C 5074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 58.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 52 through 76 removed outlier: 4.630A pdb=" N GLY A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 83 through 104 Processing helix chain 'A' and resid 120 through 128 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 153 through 179 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 192 through 205 Proline residue: A 197 - end of helix removed outlier: 3.556A pdb=" N SER A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.317A pdb=" N SER A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.589A pdb=" N ALA A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 352 Processing helix chain 'A' and resid 360 through 380 Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.802A pdb=" N GLY A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 432 through 454 removed outlier: 4.054A pdb=" N ASN A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 484 Proline residue: A 479 - end of helix Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'B' and resid 52 through 76 removed outlier: 4.630A pdb=" N GLY B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 104 Processing helix chain 'B' and resid 120 through 128 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 153 through 179 Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 192 through 205 Proline residue: B 197 - end of helix removed outlier: 3.556A pdb=" N SER B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.317A pdb=" N SER B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.589A pdb=" N ALA B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 352 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 398 removed outlier: 3.802A pdb=" N GLY B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 432 through 454 removed outlier: 4.054A pdb=" N ASN B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 484 Proline residue: B 479 - end of helix Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 513 through 521 394 hydrogen bonds defined for protein. 1182 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: 2.27 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1816 1.33 - 1.45: 1622 1.45 - 1.57: 4398 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7936 Sorted by residual: bond pdb=" C1 ASC A 703 " pdb=" O4 ASC A 703 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 ASC B 703 " pdb=" O4 ASC B 703 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" CG PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 1.503 1.369 0.134 3.40e-02 8.65e+02 1.55e+01 bond pdb=" CG PRO B 197 " pdb=" CD PRO B 197 " ideal model delta sigma weight residual 1.503 1.369 0.134 3.40e-02 8.65e+02 1.55e+01 bond pdb=" CG1 ILE A 93 " pdb=" CD1 ILE A 93 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.16e+00 ... (remaining 7931 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.06: 182 104.06 - 111.64: 3476 111.64 - 119.22: 3048 119.22 - 126.79: 3996 126.79 - 134.37: 130 Bond angle restraints: 10832 Sorted by residual: angle pdb=" CA PRO B 197 " pdb=" N PRO B 197 " pdb=" CD PRO B 197 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" CA PRO A 197 " pdb=" N PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" N PRO A 197 " pdb=" CD PRO A 197 " pdb=" CG PRO A 197 " ideal model delta sigma weight residual 103.20 96.54 6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" N PRO B 197 " pdb=" CD PRO B 197 " pdb=" CG PRO B 197 " ideal model delta sigma weight residual 103.20 96.54 6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" CA THR A 196 " pdb=" CB THR A 196 " pdb=" CG2 THR A 196 " ideal model delta sigma weight residual 110.50 117.87 -7.37 1.70e+00 3.46e-01 1.88e+01 ... (remaining 10827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4206 17.46 - 34.93: 386 34.93 - 52.39: 44 52.39 - 69.86: 8 69.86 - 87.32: 4 Dihedral angle restraints: 4648 sinusoidal: 1782 harmonic: 2866 Sorted by residual: dihedral pdb=" CA LEU B 201 " pdb=" C LEU B 201 " pdb=" N ILE B 202 " pdb=" CA ILE B 202 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU A 201 " pdb=" C LEU A 201 " pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1058 0.079 - 0.157: 196 0.157 - 0.236: 14 0.236 - 0.315: 6 0.315 - 0.394: 8 Chirality restraints: 1282 Sorted by residual: chirality pdb=" C5 ASC A 703 " pdb=" C4 ASC A 703 " pdb=" C6 ASC A 703 " pdb=" O5 ASC A 703 " both_signs ideal model delta sigma weight residual False 2.26 2.65 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C5 ASC B 703 " pdb=" C4 ASC B 703 " pdb=" C6 ASC B 703 " pdb=" O5 ASC B 703 " both_signs ideal model delta sigma weight residual False 2.26 2.65 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE B 569 " pdb=" CA ILE B 569 " pdb=" CG1 ILE B 569 " pdb=" CG2 ILE B 569 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1279 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B 288 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 288 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " -0.019 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE A 262 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.000 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1450 2.76 - 3.30: 7554 3.30 - 3.83: 13718 3.83 - 4.37: 16566 4.37 - 4.90: 28239 Nonbonded interactions: 67527 Sorted by model distance: nonbonded pdb="NA NA B 701 " pdb=" O1 ASC B 703 " model vdw 2.230 2.470 nonbonded pdb="NA NA A 701 " pdb=" O1 ASC A 703 " model vdw 2.230 2.470 nonbonded pdb=" O SER A 117 " pdb=" O3 ASC A 703 " model vdw 2.273 2.440 nonbonded pdb=" O SER B 117 " pdb=" O3 ASC B 703 " model vdw 2.273 2.440 nonbonded pdb=" O CYS A 275 " pdb=" OG1 THR A 279 " model vdw 2.303 2.440 ... (remaining 67522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.810 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: 12.050 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.060 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 7936 Z= 0.567 Angle : 1.112 9.372 10832 Z= 0.586 Chirality : 0.068 0.394 1282 Planarity : 0.010 0.087 1346 Dihedral : 13.301 87.320 2814 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1002 helix: -1.97 (0.16), residues: 656 sheet: -4.36 (0.58), residues: 20 loop : -1.55 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 48 HIS 0.010 0.003 HIS A 157 PHE 0.059 0.003 PHE A 262 TYR 0.015 0.002 TYR B 143 ARG 0.007 0.001 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.786 Fit side-chains REVERT: A 212 ASP cc_start: 0.6573 (m-30) cc_final: 0.6370 (m-30) REVERT: B 212 ASP cc_start: 0.6572 (m-30) cc_final: 0.6366 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1709 time to fit residues: 24.2627 Evaluate side-chains 84 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7936 Z= 0.229 Angle : 0.632 7.655 10832 Z= 0.329 Chirality : 0.043 0.159 1282 Planarity : 0.007 0.061 1346 Dihedral : 7.512 87.528 1108 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.19 % Allowed : 8.55 % Favored : 90.26 % 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: -1.50 (0.26), residues: 1002 helix: -0.56 (0.19), residues: 660 sheet: -4.28 (0.59), residues: 20 loop : -1.40 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 146 HIS 0.007 0.001 HIS A 157 PHE 0.020 0.001 PHE A 262 TYR 0.008 0.001 TYR B 481 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.856 Fit side-chains REVERT: A 148 MET cc_start: 0.6129 (mmm) cc_final: 0.5870 (mmm) REVERT: B 148 MET cc_start: 0.6125 (mmm) cc_final: 0.5865 (mmm) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.1521 time to fit residues: 22.6468 Evaluate side-chains 100 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 508 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7936 Z= 0.316 Angle : 0.659 7.543 10832 Z= 0.340 Chirality : 0.046 0.172 1282 Planarity : 0.006 0.054 1346 Dihedral : 7.229 87.046 1108 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.43 % Allowed : 10.93 % Favored : 87.65 % 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: -1.08 (0.26), residues: 1002 helix: -0.09 (0.19), residues: 644 sheet: -4.20 (0.62), residues: 20 loop : -1.56 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 534 HIS 0.005 0.002 HIS B 157 PHE 0.017 0.002 PHE B 262 TYR 0.010 0.001 TYR B 481 ARG 0.003 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.819 Fit side-chains REVERT: A 85 MET cc_start: 0.8575 (tmm) cc_final: 0.8365 (tmm) REVERT: A 148 MET cc_start: 0.6196 (mmm) cc_final: 0.5959 (mmm) REVERT: B 85 MET cc_start: 0.8577 (tmm) cc_final: 0.8366 (tmm) REVERT: B 148 MET cc_start: 0.6192 (mmm) cc_final: 0.5953 (mmm) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.1454 time to fit residues: 23.4338 Evaluate side-chains 104 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 508 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 43 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7936 Z= 0.212 Angle : 0.592 7.213 10832 Z= 0.304 Chirality : 0.043 0.156 1282 Planarity : 0.006 0.052 1346 Dihedral : 6.810 87.386 1108 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.90 % Allowed : 13.06 % Favored : 85.04 % 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: -0.55 (0.27), residues: 1002 helix: 0.38 (0.20), residues: 646 sheet: -4.02 (0.68), residues: 20 loop : -1.49 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.004 0.001 HIS A 157 PHE 0.010 0.001 PHE B 262 TYR 0.008 0.001 TYR B 481 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.874 Fit side-chains REVERT: A 414 MET cc_start: 0.7877 (mtt) cc_final: 0.7639 (mtt) REVERT: B 414 MET cc_start: 0.7877 (mtt) cc_final: 0.7641 (mtt) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.1318 time to fit residues: 21.6715 Evaluate side-chains 100 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0770 chunk 71 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7936 Z= 0.222 Angle : 0.589 7.133 10832 Z= 0.303 Chirality : 0.044 0.162 1282 Planarity : 0.006 0.050 1346 Dihedral : 6.703 87.341 1108 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.61 % Allowed : 13.78 % Favored : 83.61 % 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: -0.29 (0.27), residues: 1002 helix: 0.61 (0.20), residues: 646 sheet: -4.17 (0.68), residues: 20 loop : -1.41 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 134 HIS 0.005 0.001 HIS B 157 PHE 0.011 0.001 PHE B 566 TYR 0.008 0.001 TYR A 481 ARG 0.001 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.830 Fit side-chains REVERT: A 414 MET cc_start: 0.7844 (mtt) cc_final: 0.7633 (mtt) REVERT: A 434 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7447 (mp) REVERT: B 414 MET cc_start: 0.7842 (mtt) cc_final: 0.7634 (mtt) REVERT: B 434 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7443 (mp) outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.1282 time to fit residues: 20.7665 Evaluate side-chains 96 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7936 Z= 0.252 Angle : 0.604 7.138 10832 Z= 0.310 Chirality : 0.044 0.165 1282 Planarity : 0.006 0.049 1346 Dihedral : 6.739 89.455 1108 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.33 % Allowed : 14.25 % Favored : 82.42 % 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: -0.23 (0.27), residues: 1002 helix: 0.65 (0.20), residues: 646 sheet: -4.22 (0.69), residues: 20 loop : -1.38 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 134 HIS 0.005 0.001 HIS B 157 PHE 0.013 0.001 PHE B 207 TYR 0.008 0.001 TYR A 481 ARG 0.002 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.851 Fit side-chains REVERT: A 104 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: A 168 MET cc_start: 0.7462 (mmm) cc_final: 0.7158 (mmm) REVERT: A 414 MET cc_start: 0.7847 (mtt) cc_final: 0.7631 (mtt) REVERT: A 434 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7457 (mp) REVERT: B 104 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6931 (mt0) REVERT: B 168 MET cc_start: 0.7456 (mmm) cc_final: 0.7159 (mmm) REVERT: B 414 MET cc_start: 0.7846 (mtt) cc_final: 0.7632 (mtt) REVERT: B 434 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7453 (mp) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.1266 time to fit residues: 24.0651 Evaluate side-chains 112 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7936 Z= 0.264 Angle : 0.610 7.151 10832 Z= 0.313 Chirality : 0.045 0.165 1282 Planarity : 0.006 0.050 1346 Dihedral : 6.748 90.631 1108 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.61 % Allowed : 15.20 % Favored : 82.19 % 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: -0.17 (0.27), residues: 1002 helix: 0.68 (0.20), residues: 648 sheet: -4.22 (0.69), residues: 20 loop : -1.33 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 134 HIS 0.005 0.001 HIS B 157 PHE 0.014 0.001 PHE B 207 TYR 0.008 0.001 TYR B 481 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.838 Fit side-chains REVERT: A 104 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6935 (mt0) REVERT: A 414 MET cc_start: 0.7846 (mtt) cc_final: 0.7640 (mtt) REVERT: A 434 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7481 (mp) REVERT: B 104 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: B 414 MET cc_start: 0.7846 (mtt) cc_final: 0.7640 (mtt) REVERT: B 434 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7475 (mp) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.1358 time to fit residues: 24.4272 Evaluate side-chains 116 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.0040 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7936 Z= 0.250 Angle : 0.603 7.110 10832 Z= 0.309 Chirality : 0.044 0.163 1282 Planarity : 0.006 0.050 1346 Dihedral : 6.691 90.804 1108 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.85 % Allowed : 15.20 % Favored : 81.95 % 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: -0.10 (0.27), residues: 1002 helix: 0.76 (0.20), residues: 646 sheet: -4.22 (0.67), residues: 20 loop : -1.35 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.005 0.001 HIS B 157 PHE 0.013 0.001 PHE B 207 TYR 0.008 0.001 TYR A 481 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.961 Fit side-chains REVERT: A 104 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6845 (mt0) REVERT: A 168 MET cc_start: 0.7539 (mmm) cc_final: 0.7231 (mmm) REVERT: A 414 MET cc_start: 0.7781 (mtt) cc_final: 0.7574 (mtt) REVERT: A 434 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7466 (mp) REVERT: B 104 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: B 168 MET cc_start: 0.7537 (mmm) cc_final: 0.7232 (mmm) REVERT: B 414 MET cc_start: 0.7778 (mtt) cc_final: 0.7573 (mtt) REVERT: B 434 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7461 (mp) outliers start: 24 outliers final: 16 residues processed: 116 average time/residue: 0.1614 time to fit residues: 29.8470 Evaluate side-chains 108 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7936 Z= 0.238 Angle : 0.597 7.083 10832 Z= 0.306 Chirality : 0.044 0.160 1282 Planarity : 0.006 0.050 1346 Dihedral : 6.652 90.894 1108 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.38 % Allowed : 15.44 % Favored : 82.19 % 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: -0.06 (0.27), residues: 1002 helix: 0.82 (0.20), residues: 648 sheet: -4.17 (0.67), residues: 20 loop : -1.41 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.005 0.001 HIS A 157 PHE 0.012 0.001 PHE A 207 TYR 0.008 0.001 TYR A 481 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.839 Fit side-chains REVERT: A 104 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6877 (mt0) REVERT: A 168 MET cc_start: 0.7474 (mmm) cc_final: 0.7150 (mmm) REVERT: A 414 MET cc_start: 0.7768 (mtt) cc_final: 0.7567 (mtt) REVERT: A 434 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7458 (mp) REVERT: B 104 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: B 168 MET cc_start: 0.7472 (mmm) cc_final: 0.7153 (mmm) REVERT: B 434 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7457 (mp) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.1315 time to fit residues: 22.7014 Evaluate side-chains 108 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.0030 chunk 99 optimal weight: 0.0470 chunk 91 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7936 Z= 0.183 Angle : 0.560 6.864 10832 Z= 0.286 Chirality : 0.042 0.155 1282 Planarity : 0.005 0.049 1346 Dihedral : 6.358 88.613 1108 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.38 % Allowed : 15.68 % Favored : 81.95 % 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: 0.17 (0.28), residues: 1002 helix: 0.97 (0.20), residues: 662 sheet: -4.23 (0.66), residues: 20 loop : -1.36 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.004 0.001 HIS A 157 PHE 0.008 0.001 PHE A 262 TYR 0.008 0.001 TYR A 481 ARG 0.001 0.000 ARG B 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.799 Fit side-chains REVERT: A 104 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6754 (mt0) REVERT: A 168 MET cc_start: 0.7358 (mmm) cc_final: 0.7107 (mmm) REVERT: A 434 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7403 (mp) REVERT: B 104 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6790 (mt0) REVERT: B 168 MET cc_start: 0.7357 (mmm) cc_final: 0.7112 (mmm) REVERT: B 434 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7401 (mp) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.1303 time to fit residues: 22.5151 Evaluate side-chains 102 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152527 restraints weight = 7308.299| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.35 r_work: 0.3733 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7936 Z= 0.254 Angle : 0.600 7.084 10832 Z= 0.308 Chirality : 0.045 0.218 1282 Planarity : 0.006 0.049 1346 Dihedral : 6.556 90.843 1108 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.38 % Allowed : 16.51 % Favored : 81.12 % 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: 0.00 (0.27), residues: 1002 helix: 0.86 (0.20), residues: 660 sheet: -4.25 (0.67), residues: 20 loop : -1.45 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 534 HIS 0.005 0.002 HIS B 157 PHE 0.015 0.001 PHE B 207 TYR 0.007 0.001 TYR A 481 ARG 0.002 0.000 ARG B 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.38 seconds wall clock time: 37 minutes 50.93 seconds (2270.93 seconds total)