Starting phenix.real_space_refine on Sat Dec 28 05:04:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytw_34094/12_2024/7ytw_34094.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytw_34094/12_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/cci-nas-00/data/ceres_data/7ytw_34094/12_2024/7ytw_34094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytw_34094/12_2024/7ytw_34094.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytw_34094/12_2024/7ytw_34094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytw_34094/12_2024/7ytw_34094.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 4 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: "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: "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} Restraints were copied for chains: B Time building chain proxies: 7.95, per 1000 atoms: 1.03 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 40 helices and 0 sheets defined 64.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.928A pdb=" N GLY A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) 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 82 through 105 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.592A pdb=" N ALA A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 180 removed outlier: 3.653A pdb=" N TRP A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 3.730A pdb=" N MET A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 191 through 204 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.546A pdb=" N LEU A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) 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 324 through 353 Processing helix chain 'A' and resid 359 through 381 Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.802A pdb=" N GLY A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 4.080A pdb=" N VAL A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 462 through 485 Proline residue: A 479 - end of helix Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.586A pdb=" N VAL A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.928A pdb=" N GLY B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) 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 82 through 105 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.592A pdb=" N ALA B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 180 removed outlier: 3.653A pdb=" N TRP B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Proline residue: B 158 - end of helix removed outlier: 3.730A pdb=" N MET B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 191 through 204 Proline residue: B 197 - end of helix Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.546A pdb=" N LEU B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) 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 324 through 353 Processing helix chain 'B' and resid 359 through 381 Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.802A pdb=" N GLY B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 4.080A pdb=" N VAL B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 462 through 485 Proline residue: B 479 - end of helix Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 512 through 522 removed outlier: 3.586A pdb=" N VAL B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1344 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: 1.96 Time building geometry restraints manager: 2.25 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: 0.00 - 1.87: 10088 1.87 - 3.75: 570 3.75 - 5.62: 104 5.62 - 7.50: 48 7.50 - 9.37: 22 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: 4204 17.46 - 34.93: 386 34.93 - 52.39: 44 52.39 - 69.86: 7 69.86 - 87.32: 4 Dihedral angle restraints: 4645 sinusoidal: 1779 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 4642 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: 2.03 - 2.60: 101 2.60 - 3.18: 6476 3.18 - 3.75: 12980 3.75 - 4.33: 17970 4.33 - 4.90: 29787 Nonbonded interactions: 67314 Sorted by model distance: nonbonded pdb=" SG CYS B 78 " pdb=" SG CYS B 136 " model vdw 2.029 3.760 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 3.040 nonbonded pdb=" O SER B 117 " pdb=" O3 ASC B 703 " model vdw 2.273 3.040 ... (remaining 67309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.730 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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= 0.566 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 : 2.029 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 to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.840 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: 0.2102 time to fit residues: 29.3967 Evaluate side-chains 84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 0.0000 chunk 42 optimal weight: 0.0970 chunk 25 optimal weight: 0.0000 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 overall best weight: 0.2386 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7936 Z= 0.214 Angle : 0.653 7.772 10832 Z= 0.343 Chirality : 0.044 0.158 1282 Planarity : 0.007 0.062 1346 Dihedral : 7.746 88.909 1108 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.95 % Allowed : 7.36 % Favored : 91.69 % 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: -1.33 (0.25), residues: 1002 helix: -0.49 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 146 HIS 0.006 0.001 HIS A 157 PHE 0.020 0.001 PHE A 262 TYR 0.009 0.001 TYR B 481 ARG 0.002 0.000 ARG B 529 *********************** 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 98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.885 Fit side-chains REVERT: A 148 MET cc_start: 0.6145 (mmm) cc_final: 0.5868 (mmm) REVERT: B 148 MET cc_start: 0.6142 (mmm) cc_final: 0.5865 (mmm) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1577 time to fit residues: 22.2934 Evaluate side-chains 92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR 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: 0.0970 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.1434 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= 0.219 Angle : 0.607 7.386 10832 Z= 0.316 Chirality : 0.044 0.169 1282 Planarity : 0.006 0.054 1346 Dihedral : 7.247 83.164 1108 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -0.48 (0.26), residues: 1002 helix: 0.27 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 156 HIS 0.004 0.001 HIS A 157 PHE 0.016 0.001 PHE A 262 TYR 0.010 0.001 TYR B 481 ARG 0.002 0.000 ARG B 236 *********************** 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 104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.828 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 0.1553 time to fit residues: 23.9055 Evaluate side-chains 95 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7936 Z= 0.248 Angle : 0.616 7.222 10832 Z= 0.320 Chirality : 0.045 0.172 1282 Planarity : 0.006 0.052 1346 Dihedral : 7.095 81.277 1108 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.19 % Allowed : 13.06 % Favored : 85.75 % 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: -0.21 (0.27), residues: 1002 helix: 0.48 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 156 HIS 0.004 0.001 HIS B 157 PHE 0.013 0.001 PHE A 262 TYR 0.009 0.001 TYR A 481 ARG 0.002 0.000 ARG B 529 *********************** 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 98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.949 Fit side-chains REVERT: A 434 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 559 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4305 (tmm) REVERT: B 434 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7445 (mp) REVERT: B 559 MET cc_start: 0.4845 (OUTLIER) cc_final: 0.4304 (tmm) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.1867 time to fit residues: 27.7585 Evaluate side-chains 93 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 434 ILE 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 434 ILE 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: 1.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.1695 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= 0.269 Angle : 0.623 7.190 10832 Z= 0.322 Chirality : 0.045 0.178 1282 Planarity : 0.006 0.053 1346 Dihedral : 7.131 81.031 1108 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 13.42 % Favored : 84.68 % 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: 0.56 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.23 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 309 HIS 0.004 0.001 HIS A 157 PHE 0.015 0.001 PHE B 207 TYR 0.008 0.001 TYR A 481 ARG 0.002 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 102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.849 Fit side-chains REVERT: A 434 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 480 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6887 (m-40) REVERT: A 559 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4332 (tmm) REVERT: B 434 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (mp) REVERT: B 480 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6887 (m-40) REVERT: B 559 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4331 (tmm) outliers start: 16 outliers final: 8 residues processed: 100 average time/residue: 0.1505 time to fit residues: 22.9438 Evaluate side-chains 100 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 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 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR 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 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.0060 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.0030 chunk 10 optimal weight: 0.5980 overall best weight: 0.2204 ------------------------------------------------------------------------------- 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: 0.7438 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7936 Z= 0.191 Angle : 0.575 6.701 10832 Z= 0.297 Chirality : 0.043 0.163 1282 Planarity : 0.006 0.052 1346 Dihedral : 6.754 82.633 1108 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.90 % Allowed : 13.54 % Favored : 84.56 % 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: 0.26 (0.27), residues: 1002 helix: 0.87 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.18 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 134 HIS 0.003 0.001 HIS A 157 PHE 0.012 0.001 PHE B 566 TYR 0.008 0.001 TYR A 481 ARG 0.001 0.000 ARG B 562 *********************** 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 101 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.839 Fit side-chains REVERT: A 168 MET cc_start: 0.7495 (mmm) cc_final: 0.7227 (mmm) REVERT: A 434 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 480 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6794 (m-40) REVERT: B 168 MET cc_start: 0.7496 (mmm) cc_final: 0.7234 (mmm) REVERT: B 434 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7390 (mp) REVERT: B 480 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6795 (m-40) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.1505 time to fit residues: 22.6607 Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 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** ** 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: 0.7518 moved from start: 0.1930 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= 0.268 Angle : 0.645 11.990 10832 Z= 0.328 Chirality : 0.045 0.173 1282 Planarity : 0.006 0.052 1346 Dihedral : 6.943 80.303 1108 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.54 % Allowed : 15.20 % Favored : 83.25 % 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: 0.25 (0.27), residues: 1002 helix: 0.83 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 534 HIS 0.003 0.001 HIS B 361 PHE 0.014 0.001 PHE A 207 TYR 0.008 0.001 TYR B 143 ARG 0.002 0.000 ARG A 529 *********************** 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 92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.825 Fit side-chains REVERT: A 168 MET cc_start: 0.7491 (mmm) cc_final: 0.7219 (mmm) REVERT: A 434 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 480 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6849 (m-40) REVERT: B 168 MET cc_start: 0.7494 (mmm) cc_final: 0.7229 (mmm) REVERT: B 434 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7442 (mp) REVERT: B 480 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6850 (m-40) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.1513 time to fit residues: 21.0381 Evaluate side-chains 91 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.0170 chunk 87 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7511 moved from start: 0.1958 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= 0.247 Angle : 0.610 6.927 10832 Z= 0.314 Chirality : 0.045 0.169 1282 Planarity : 0.006 0.053 1346 Dihedral : 6.978 82.164 1108 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.90 % Allowed : 14.96 % Favored : 83.14 % 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: 0.33 (0.27), residues: 1002 helix: 0.86 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 534 HIS 0.004 0.001 HIS A 157 PHE 0.012 0.001 PHE B 207 TYR 0.008 0.001 TYR B 143 ARG 0.002 0.000 ARG B 529 *********************** 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 99 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.883 Fit side-chains REVERT: A 434 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 480 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6853 (m-40) REVERT: B 434 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 480 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6865 (m-40) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.1494 time to fit residues: 22.5229 Evaluate side-chains 95 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.2042 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= 0.237 Angle : 0.634 12.907 10832 Z= 0.321 Chirality : 0.045 0.225 1282 Planarity : 0.006 0.052 1346 Dihedral : 6.920 82.487 1108 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 15.68 % 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: 0.37 (0.27), residues: 1002 helix: 0.88 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 534 HIS 0.003 0.001 HIS A 157 PHE 0.011 0.001 PHE A 207 TYR 0.008 0.001 TYR A 481 ARG 0.002 0.000 ARG B 562 *********************** 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 97 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.825 Fit side-chains REVERT: A 168 MET cc_start: 0.7577 (mmm) cc_final: 0.7329 (mmm) REVERT: A 434 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (mp) REVERT: A 480 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6829 (m-40) REVERT: B 168 MET cc_start: 0.7576 (mmm) cc_final: 0.7335 (mmm) REVERT: B 434 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7447 (mp) REVERT: B 480 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6836 (m-40) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.1510 time to fit residues: 22.4923 Evaluate side-chains 95 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.2052 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= 0.246 Angle : 0.635 11.914 10832 Z= 0.322 Chirality : 0.045 0.209 1282 Planarity : 0.006 0.053 1346 Dihedral : 6.911 82.800 1108 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.90 % Allowed : 15.68 % 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: 0.37 (0.27), residues: 1002 helix: 0.88 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.96 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 534 HIS 0.004 0.001 HIS A 157 PHE 0.013 0.001 PHE A 207 TYR 0.008 0.001 TYR A 481 ARG 0.001 0.000 ARG A 529 ********************** 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 99 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.790 Fit side-chains REVERT: A 168 MET cc_start: 0.7579 (mmm) cc_final: 0.7324 (mmm) REVERT: A 434 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 480 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6827 (m-40) REVERT: B 168 MET cc_start: 0.7579 (mmm) cc_final: 0.7334 (mmm) REVERT: B 434 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 480 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6828 (m-40) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.1506 time to fit residues: 22.5120 Evaluate side-chains 97 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150961 restraints weight = 7289.928| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.32 r_work: 0.3706 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2056 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= 0.266 Angle : 0.642 11.682 10832 Z= 0.326 Chirality : 0.046 0.204 1282 Planarity : 0.006 0.053 1346 Dihedral : 6.983 82.969 1108 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.66 % Allowed : 16.39 % 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: 0.34 (0.27), residues: 1002 helix: 0.84 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 534 HIS 0.004 0.001 HIS A 157 PHE 0.015 0.001 PHE A 207 TYR 0.008 0.001 TYR A 481 ARG 0.001 0.000 ARG B 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.35 seconds wall clock time: 36 minutes 12.32 seconds (2172.32 seconds total)