Starting phenix.real_space_refine on Thu Jul 2 08:12:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_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_34094/07_2026/7ytw_34094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ytw_34094/07_2026/7ytw_34094.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.51, per 1000 atoms: 0.32 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 - 3.00 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: 0.75 Conformation dependent library (CDL) restraints added in 475.2 milliseconds 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: 0.19 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: 1.22 Time building geometry restraints manager: 1.01 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 - 15.14: 4042 15.14 - 30.27: 480 30.27 - 45.41: 86 45.41 - 60.55: 10 60.55 - 75.69: 2 Dihedral angle restraints: 4620 sinusoidal: 1754 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 4617 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: 1442 2.76 - 3.30: 7518 3.30 - 3.83: 13648 3.83 - 4.37: 16474 4.37 - 4.90: 28229 Nonbonded interactions: 67311 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 3.040 nonbonded pdb=" O SER B 117 " pdb=" O3 ASC B 703 " model vdw 2.273 3.040 nonbonded pdb=" O CYS A 275 " pdb=" OG1 THR A 279 " model vdw 2.303 3.040 ... (remaining 67306 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: 0.02 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: 5.010 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 7938 Z= 0.342 Angle : 1.112 9.372 10836 Z= 0.586 Chirality : 0.068 0.394 1282 Planarity : 0.010 0.087 1346 Dihedral : 12.981 75.687 2786 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG B 463 TYR 0.015 0.002 TYR B 143 PHE 0.059 0.003 PHE A 262 TRP 0.014 0.002 TRP A 48 HIS 0.010 0.003 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.34 ( 7936) covalent geometry : angle 1.11218 / 0.59 (10832) SS BOND : bond 0.00243 / 0.12 ( 2) SS BOND : angle 0.96212 / 0.53 ( 4) hydrogen bonds : bond 0.14790 / 9.94 ( 448) hydrogen bonds : angle 6.81052 / 4.82 ( 1344) *********************** 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 : 0.270 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: 0.0686 time to fit residues: 9.8947 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151322 restraints weight = 7331.273| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.33 r_work: 0.3719 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7938 Z= 0.179 Angle : 0.682 8.114 10836 Z= 0.357 Chirality : 0.045 0.165 1282 Planarity : 0.007 0.062 1346 Dihedral : 5.502 21.765 1080 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.95 % Allowed : 8.31 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.25), residues: 1002 helix: -0.62 (0.18), residues: 672 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 529 TYR 0.010 0.001 TYR B 481 PHE 0.021 0.002 PHE A 262 TRP 0.004 0.001 TRP A 146 HIS 0.006 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 7936) covalent geometry : angle 0.68198 / 0.36 (10832) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 1.29408 / 0.68 ( 4) hydrogen bonds : bond 0.05620 / 3.96 ( 448) hydrogen bonds : angle 4.85134 / 3.49 ( 1344) *********************** 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 to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.263 Fit side-chains REVERT: A 148 MET cc_start: 0.6592 (mmm) cc_final: 0.6105 (mmm) REVERT: A 168 MET cc_start: 0.7757 (mmm) cc_final: 0.7419 (mmm) REVERT: B 148 MET cc_start: 0.6589 (mmm) cc_final: 0.6110 (mmm) REVERT: B 168 MET cc_start: 0.7776 (mmm) cc_final: 0.7437 (mmm) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.0663 time to fit residues: 9.7180 Evaluate side-chains 98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 79 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.4034 r_free = 0.4034 target = 0.175530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151171 restraints weight = 7330.077| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.34 r_work: 0.3725 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7938 Z= 0.174 Angle : 0.645 7.654 10836 Z= 0.336 Chirality : 0.045 0.170 1282 Planarity : 0.006 0.055 1346 Dihedral : 5.224 21.026 1080 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.66 % Allowed : 11.88 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1002 helix: 0.06 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.011 0.001 TYR B 481 PHE 0.016 0.001 PHE A 262 TRP 0.004 0.001 TRP A 534 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 7936) covalent geometry : angle 0.64449 / 0.34 (10832) SS BOND : bond 0.00046 / 0.02 ( 2) SS BOND : angle 1.11697 / 0.59 ( 4) hydrogen bonds : bond 0.05306 / 3.70 ( 448) hydrogen bonds : angle 4.55370 / 3.25 ( 1344) *********************** 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 106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.195 Fit side-chains REVERT: A 148 MET cc_start: 0.6510 (mmm) cc_final: 0.6106 (mmm) REVERT: A 434 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 148 MET cc_start: 0.6496 (mmm) cc_final: 0.6105 (mmm) REVERT: B 434 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7734 (mp) outliers start: 14 outliers final: 6 residues processed: 104 average time/residue: 0.0515 time to fit residues: 8.3677 Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 A residue 434 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4034 r_free = 0.4034 target = 0.175792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151442 restraints weight = 7405.575| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.35 r_work: 0.3718 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7938 Z= 0.167 Angle : 0.632 7.260 10836 Z= 0.328 Chirality : 0.045 0.172 1282 Planarity : 0.006 0.052 1346 Dihedral : 5.046 21.135 1080 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.14 % Allowed : 13.06 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1002 helix: 0.38 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.009 0.001 TYR A 481 PHE 0.015 0.001 PHE B 207 TRP 0.003 0.001 TRP B 134 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7936) covalent geometry : angle 0.63190 / 0.33 (10832) SS BOND : bond 0.00044 / 0.02 ( 2) SS BOND : angle 1.02330 / 0.55 ( 4) hydrogen bonds : bond 0.05103 / 3.56 ( 448) hydrogen bonds : angle 4.47848 / 3.20 ( 1344) *********************** 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 100 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.179 Fit side-chains REVERT: A 148 MET cc_start: 0.6520 (mmm) cc_final: 0.6100 (mmm) REVERT: A 480 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7087 (m-40) REVERT: A 559 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4654 (tmm) REVERT: B 148 MET cc_start: 0.6514 (mmm) cc_final: 0.6107 (mmm) REVERT: B 480 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7076 (m-40) REVERT: B 559 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4660 (tmm) outliers start: 18 outliers final: 8 residues processed: 96 average time/residue: 0.0485 time to fit residues: 7.6237 Evaluate side-chains 92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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 480 ASN Chi-restraints excluded: chain B residue 491 THR 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 94 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 87 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4052 r_free = 0.4052 target = 0.177656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153525 restraints weight = 7349.727| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.34 r_work: 0.3749 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7938 Z= 0.149 Angle : 0.605 7.008 10836 Z= 0.313 Chirality : 0.044 0.168 1282 Planarity : 0.006 0.051 1346 Dihedral : 4.909 20.863 1080 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.90 % Allowed : 14.73 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1002 helix: 0.61 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.23 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.009 0.001 TYR A 481 PHE 0.013 0.001 PHE B 207 TRP 0.003 0.001 TRP B 134 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7936) covalent geometry : angle 0.60425 / 0.31 (10832) SS BOND : bond 0.00091 / 0.05 ( 2) SS BOND : angle 1.20822 / 0.71 ( 4) hydrogen bonds : bond 0.04919 / 3.44 ( 448) hydrogen bonds : angle 4.39369 / 3.15 ( 1344) *********************** 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 98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.284 Fit side-chains REVERT: A 148 MET cc_start: 0.6465 (mmm) cc_final: 0.6109 (mmm) REVERT: A 168 MET cc_start: 0.7804 (mmm) cc_final: 0.7464 (mmm) REVERT: A 434 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 480 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7086 (m-40) REVERT: A 559 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4666 (tmm) REVERT: B 148 MET cc_start: 0.6453 (mmm) cc_final: 0.6110 (mmm) REVERT: B 168 MET cc_start: 0.7802 (mmm) cc_final: 0.7462 (mmm) REVERT: B 434 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7713 (mp) REVERT: B 480 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7083 (m-40) REVERT: B 559 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.4671 (tmm) outliers start: 16 outliers final: 8 residues processed: 96 average time/residue: 0.0618 time to fit residues: 9.1389 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 : 0.196 ------------------------------------------------------------------------------- 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 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 320 LEU 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 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 53 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4055 r_free = 0.4055 target = 0.178003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153817 restraints weight = 7335.758| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.34 r_work: 0.3744 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7938 Z= 0.149 Angle : 0.601 6.943 10836 Z= 0.310 Chirality : 0.044 0.170 1282 Planarity : 0.006 0.052 1346 Dihedral : 4.814 20.675 1080 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 15.44 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 1002 helix: 0.75 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.22 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.008 0.001 TYR B 481 PHE 0.013 0.001 PHE A 207 TRP 0.004 0.001 TRP A 146 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7936) covalent geometry : angle 0.60056 / 0.31 (10832) SS BOND : bond 0.00003 / 0.00 ( 2) SS BOND : angle 1.15177 / 0.64 ( 4) hydrogen bonds : bond 0.04862 / 3.39 ( 448) hydrogen bonds : angle 4.35854 / 3.12 ( 1344) *********************** 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 94 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.256 Fit side-chains REVERT: A 148 MET cc_start: 0.6402 (mmm) cc_final: 0.6054 (mmm) REVERT: A 434 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7696 (mp) REVERT: A 480 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: A 559 MET cc_start: 0.5257 (OUTLIER) cc_final: 0.4778 (tmm) REVERT: B 148 MET cc_start: 0.6373 (mmm) cc_final: 0.6045 (mmm) REVERT: B 434 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 480 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7047 (m-40) REVERT: B 559 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4771 (tmm) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.0553 time to fit residues: 7.7547 Evaluate side-chains 94 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 375 ILE 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 375 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 76 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4047 r_free = 0.4047 target = 0.177259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152941 restraints weight = 7380.112| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.35 r_work: 0.3729 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7938 Z= 0.155 Angle : 0.608 6.905 10836 Z= 0.314 Chirality : 0.045 0.168 1282 Planarity : 0.006 0.052 1346 Dihedral : 4.790 20.591 1080 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.61 % Allowed : 15.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.27), residues: 1002 helix: 0.76 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.008 0.001 TYR A 481 PHE 0.013 0.001 PHE A 207 TRP 0.003 0.001 TRP B 534 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7936) covalent geometry : angle 0.60756 / 0.31 (10832) SS BOND : bond 0.00030 / 0.02 ( 2) SS BOND : angle 1.10896 / 0.62 ( 4) hydrogen bonds : bond 0.04895 / 3.42 ( 448) hydrogen bonds : angle 4.37232 / 3.13 ( 1344) *********************** 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 100 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.271 Fit side-chains REVERT: A 104 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: A 148 MET cc_start: 0.6330 (mmm) cc_final: 0.6013 (mmm) REVERT: A 168 MET cc_start: 0.7784 (mmm) cc_final: 0.7496 (mmm) REVERT: A 434 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 480 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7068 (m-40) REVERT: A 559 MET cc_start: 0.5181 (OUTLIER) cc_final: 0.4806 (tmm) REVERT: B 104 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: B 148 MET cc_start: 0.6312 (mmm) cc_final: 0.6009 (mmm) REVERT: B 168 MET cc_start: 0.7811 (mmm) cc_final: 0.7522 (mmm) REVERT: B 434 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 480 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7068 (m-40) REVERT: B 559 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.4801 (tmm) outliers start: 22 outliers final: 10 residues processed: 98 average time/residue: 0.0589 time to fit residues: 8.8428 Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN 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 A residue 559 MET Chi-restraints excluded: chain B residue 104 GLN 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 Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 75 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155539 restraints weight = 7326.653| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.35 r_work: 0.3763 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7938 Z= 0.138 Angle : 0.586 6.738 10836 Z= 0.303 Chirality : 0.044 0.169 1282 Planarity : 0.006 0.052 1346 Dihedral : 4.671 20.446 1080 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.38 % Allowed : 16.39 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 1002 helix: 0.86 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 529 TYR 0.008 0.001 TYR A 481 PHE 0.010 0.001 PHE B 207 TRP 0.004 0.001 TRP B 134 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7936) covalent geometry : angle 0.58615 / 0.30 (10832) SS BOND : bond 0.00031 / 0.02 ( 2) SS BOND : angle 1.08022 / 0.60 ( 4) hydrogen bonds : bond 0.04708 / 3.28 ( 448) hydrogen bonds : angle 4.29765 / 3.08 ( 1344) *********************** 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 102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.195 Fit side-chains REVERT: A 104 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: A 148 MET cc_start: 0.6301 (mmm) cc_final: 0.6056 (mmm) REVERT: A 168 MET cc_start: 0.7715 (mmm) cc_final: 0.7431 (mmm) REVERT: A 434 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 559 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4983 (tmm) REVERT: B 104 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: B 148 MET cc_start: 0.6292 (mmm) cc_final: 0.6056 (mmm) REVERT: B 168 MET cc_start: 0.7755 (mmm) cc_final: 0.7469 (mmm) REVERT: B 434 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7695 (mp) REVERT: B 559 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.4972 (tmm) outliers start: 20 outliers final: 10 residues processed: 100 average time/residue: 0.0595 time to fit residues: 9.1121 Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN 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 491 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 104 GLN 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 491 THR Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4053 r_free = 0.4053 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153415 restraints weight = 7325.339| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.35 r_work: 0.3745 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7938 Z= 0.157 Angle : 0.606 6.887 10836 Z= 0.313 Chirality : 0.046 0.234 1282 Planarity : 0.006 0.052 1346 Dihedral : 4.722 20.439 1080 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.85 % Allowed : 16.15 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 1002 helix: 0.82 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.10 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.008 0.001 TYR B 481 PHE 0.013 0.001 PHE A 207 TRP 0.006 0.001 TRP B 534 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7936) covalent geometry : angle 0.60616 / 0.31 (10832) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 1.07288 / 0.59 ( 4) hydrogen bonds : bond 0.04855 / 3.38 ( 448) hydrogen bonds : angle 4.37445 / 3.14 ( 1344) *********************** 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 102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.210 Fit side-chains REVERT: A 104 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: A 148 MET cc_start: 0.6268 (mmm) cc_final: 0.6062 (mmm) REVERT: A 168 MET cc_start: 0.7824 (mmm) cc_final: 0.7570 (mmm) REVERT: A 434 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 480 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7072 (m-40) REVERT: A 559 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.4978 (tmm) REVERT: B 104 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: B 168 MET cc_start: 0.7843 (mmm) cc_final: 0.7593 (mmm) REVERT: B 434 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7710 (mp) REVERT: B 480 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7065 (m-40) REVERT: B 559 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.4966 (tmm) outliers start: 24 outliers final: 14 residues processed: 100 average time/residue: 0.0683 time to fit residues: 10.4105 Evaluate side-chains 98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN 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 320 LEU 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 480 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 104 GLN 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 320 LEU 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 480 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.171654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148057 restraints weight = 7378.390| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.23 r_work: 0.3674 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7938 Z= 0.203 Angle : 0.657 7.256 10836 Z= 0.340 Chirality : 0.047 0.203 1282 Planarity : 0.006 0.053 1346 Dihedral : 4.937 20.580 1080 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.85 % Allowed : 16.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.27), residues: 1002 helix: 0.62 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 463 TYR 0.008 0.001 TYR B 314 PHE 0.018 0.002 PHE A 207 TRP 0.006 0.001 TRP B 534 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 ( 7936) covalent geometry : angle 0.65642 / 0.34 (10832) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 1.13938 / 0.60 ( 4) hydrogen bonds : bond 0.05246 / 3.67 ( 448) hydrogen bonds : angle 4.56189 / 3.27 ( 1344) ********************** 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 120 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.342 Fit side-chains REVERT: A 104 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: A 148 MET cc_start: 0.6307 (mmm) cc_final: 0.6080 (mmm) REVERT: A 168 MET cc_start: 0.7832 (mmm) cc_final: 0.7559 (mmm) REVERT: A 434 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 480 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7134 (m-40) REVERT: A 559 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4820 (tmm) REVERT: B 104 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: B 168 MET cc_start: 0.7829 (mmm) cc_final: 0.7561 (mmm) REVERT: B 434 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 480 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7119 (m-40) REVERT: B 559 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.4820 (tmm) outliers start: 24 outliers final: 12 residues processed: 116 average time/residue: 0.0691 time to fit residues: 12.3380 Evaluate side-chains 111 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN 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 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 A residue 559 MET Chi-restraints excluded: chain B residue 104 GLN 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 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 Chi-restraints excluded: chain B residue 559 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 90 optimal weight: 0.0570 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154419 restraints weight = 7285.590| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.23 r_work: 0.3737 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7938 Z= 0.137 Angle : 0.595 6.808 10836 Z= 0.308 Chirality : 0.045 0.206 1282 Planarity : 0.006 0.051 1346 Dihedral : 4.715 20.781 1080 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.38 % Allowed : 16.98 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1002 helix: 0.80 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.14 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 463 TYR 0.009 0.001 TYR A 481 PHE 0.010 0.001 PHE B 207 TRP 0.008 0.001 TRP A 534 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7936) covalent geometry : angle 0.59476 / 0.31 (10832) SS BOND : bond 0.00016 / 0.01 ( 2) SS BOND : angle 0.99467 / 0.59 ( 4) hydrogen bonds : bond 0.04731 / 3.30 ( 448) hydrogen bonds : angle 4.38660 / 3.15 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.19 seconds wall clock time: 32 minutes 33.61 seconds (1953.61 seconds total)