Starting phenix.real_space_refine on Tue Aug 4 22:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2026/9jhk_61485.cif" } resolution = 3.42 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= 0.012 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 42 5.49 5 S 20 5.16 5 C 4313 2.51 5 N 1139 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'DNA': 21} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.86, per 1000 atoms: 0.27 Number of scatterers: 6898 At special positions: 0 Unit cell: (72.16, 85.28, 104.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 20 16.00 P 42 15.00 O 1383 8.00 N 1139 7.00 C 4313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.63 Conformation dependent library (CDL) restraints added in 416.7 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 31.1% alpha, 17.4% beta 6 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.242A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.158A pdb=" N ASP A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.538A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.831A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.516A pdb=" N ASN A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.846A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.795A pdb=" N LEU A 67 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 27 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.671A pdb=" N VAL A 262 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.731A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.697A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU A 433 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.536A pdb=" N GLU A 411 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 463 229 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1269 1.32 - 1.44: 1927 1.44 - 1.56: 3814 1.56 - 1.69: 78 1.69 - 1.81: 35 Bond restraints: 7123 Sorted by residual: bond pdb=" C5' DG C 2 " pdb=" C4' DG C 2 " ideal model delta sigma weight residual 1.512 1.461 0.051 7.00e-03 2.04e+04 5.41e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.346 0.089 1.30e-02 5.92e+03 4.66e+01 bond pdb=" C3' DC E 8 " pdb=" O3' DC E 8 " ideal model delta sigma weight residual 1.435 1.355 0.080 1.30e-02 5.92e+03 3.79e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.48e+01 bond pdb=" C4' DA C 7 " pdb=" C3' DA C 7 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 7118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 8865 1.95 - 3.90: 795 3.90 - 5.85: 92 5.85 - 7.80: 24 7.80 - 9.75: 7 Bond angle restraints: 9783 Sorted by residual: angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 101.93 4.07 6.00e-01 2.78e+00 4.60e+01 angle pdb=" O4' DC E 7 " pdb=" C4' DC E 7 " pdb=" C3' DC E 7 " ideal model delta sigma weight residual 106.00 102.04 3.96 6.00e-01 2.78e+00 4.35e+01 angle pdb=" O4' DC E 8 " pdb=" C4' DC E 8 " pdb=" C3' DC E 8 " ideal model delta sigma weight residual 106.00 102.26 3.74 6.00e-01 2.78e+00 3.88e+01 angle pdb=" O4' DT E 12 " pdb=" C4' DT E 12 " pdb=" C3' DT E 12 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O4' DT E 9 " pdb=" C4' DT E 9 " pdb=" C3' DT E 9 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 ... (remaining 9778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 3928 25.30 - 50.59: 236 50.59 - 75.89: 40 75.89 - 101.18: 5 101.18 - 126.48: 1 Dihedral angle restraints: 4210 sinusoidal: 2023 harmonic: 2187 Sorted by residual: dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual -180.00 -144.17 -35.83 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 660 0.056 - 0.111: 291 0.111 - 0.166: 82 0.166 - 0.222: 27 0.222 - 0.277: 12 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C3' DG C 4 " pdb=" C4' DG C 4 " pdb=" O3' DG C 4 " pdb=" C2' DG C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR A 725 " pdb=" CA THR A 725 " pdb=" OG1 THR A 725 " pdb=" CG2 THR A 725 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' DT E 12 " pdb=" C4' DT E 12 " pdb=" O3' DT E 12 " pdb=" C2' DT E 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1069 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 470 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.017 2.00e-02 2.50e+03 1.56e-02 6.12e+00 pdb=" CG TRP A 623 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " -0.016 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 154 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " -0.003 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 29 2.44 - 3.06: 4273 3.06 - 3.67: 10867 3.67 - 4.29: 16318 4.29 - 4.90: 26642 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 1.829 3.340 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.846 2.320 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.858 2.320 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.874 2.320 nonbonded pdb=" ND2 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 2.005 3.420 ... (remaining 58124 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.014 0.139 7123 Z= 0.792 Angle : 1.185 9.751 9783 Z= 0.737 Chirality : 0.073 0.277 1072 Planarity : 0.007 0.053 1097 Dihedral : 16.103 126.480 2816 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.78 (0.24), residues: 743 helix: -2.90 (0.23), residues: 224 sheet: -2.50 (0.42), residues: 122 loop : -2.24 (0.25), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 721 TYR 0.034 0.004 TYR A 624 PHE 0.040 0.006 PHE A 154 TRP 0.040 0.008 TRP A 623 HIS 0.015 0.004 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.01412 / 0.79 ( 7123) covalent geometry : angle 1.18520 / 0.74 ( 9783) hydrogen bonds : bond 0.22303 / 14.53 ( 243) hydrogen bonds : angle 9.19079 / 6.14 ( 676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ILE cc_start: 0.7405 (mt) cc_final: 0.7012 (mt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0901 time to fit residues: 22.5506 Evaluate side-chains 131 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 490 GLN A 574 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053261 restraints weight = 26091.137| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 5.88 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7123 Z= 0.206 Angle : 0.860 12.259 9783 Z= 0.461 Chirality : 0.053 0.376 1072 Planarity : 0.005 0.040 1097 Dihedral : 18.969 124.409 1277 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.44 % Allowed : 12.13 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.55 (0.27), residues: 743 helix: -1.51 (0.30), residues: 226 sheet: -2.36 (0.44), residues: 113 loop : -1.54 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.019 0.002 TYR A 175 PHE 0.016 0.002 PHE A 366 TRP 0.020 0.003 TRP A 623 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 7123) covalent geometry : angle 0.86004 / 0.46 ( 9783) hydrogen bonds : bond 0.05829 / 3.71 ( 243) hydrogen bonds : angle 6.43265 / 4.46 ( 676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 85 ASN cc_start: 0.9526 (m110) cc_final: 0.9247 (m-40) REVERT: A 103 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: A 131 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8688 (mmtp) REVERT: A 191 MET cc_start: 0.9711 (mmm) cc_final: 0.9495 (mmm) REVERT: A 289 ASP cc_start: 0.8693 (t0) cc_final: 0.8247 (t0) REVERT: A 304 MET cc_start: 0.9389 (mmt) cc_final: 0.8950 (mmp) REVERT: A 353 MET cc_start: 0.8691 (ptt) cc_final: 0.8456 (ptt) REVERT: A 363 MET cc_start: 0.8957 (tpp) cc_final: 0.7967 (tpp) REVERT: A 444 LYS cc_start: 0.9666 (mttm) cc_final: 0.9353 (mmmt) REVERT: A 491 MET cc_start: 0.8772 (mtp) cc_final: 0.8463 (mtt) REVERT: A 495 LYS cc_start: 0.9717 (tttm) cc_final: 0.9437 (ttmm) REVERT: A 513 HIS cc_start: 0.9270 (m-70) cc_final: 0.8809 (m-70) REVERT: A 647 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8537 (ttmm) outliers start: 23 outliers final: 11 residues processed: 159 average time/residue: 0.0863 time to fit residues: 18.2395 Evaluate side-chains 132 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 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 = 0.3279 r_free = 0.3279 target = 0.066666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051648 restraints weight = 27103.295| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.77 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7123 Z= 0.255 Angle : 0.775 11.154 9783 Z= 0.420 Chirality : 0.050 0.273 1072 Planarity : 0.004 0.030 1097 Dihedral : 19.025 130.020 1277 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.74 % Allowed : 15.12 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.82 (0.29), residues: 743 helix: -0.79 (0.32), residues: 225 sheet: -2.16 (0.46), residues: 115 loop : -1.07 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.019 0.002 TYR A 306 PHE 0.023 0.002 PHE A 478 TRP 0.029 0.003 TRP A 482 HIS 0.007 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.26 ( 7123) covalent geometry : angle 0.77456 / 0.42 ( 9783) hydrogen bonds : bond 0.05139 / 3.32 ( 243) hydrogen bonds : angle 6.05754 / 4.16 ( 676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9673 (mmt) cc_final: 0.8871 (tpp) REVERT: A 85 ASN cc_start: 0.9534 (m110) cc_final: 0.9278 (m-40) REVERT: A 98 MET cc_start: 0.9311 (mmt) cc_final: 0.8948 (mmp) REVERT: A 131 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8775 (mmtp) REVERT: A 191 MET cc_start: 0.9723 (mmm) cc_final: 0.9466 (mmm) REVERT: A 289 ASP cc_start: 0.8858 (t0) cc_final: 0.8383 (t0) REVERT: A 295 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8647 (pt0) REVERT: A 304 MET cc_start: 0.9332 (mmt) cc_final: 0.9100 (mmp) REVERT: A 363 MET cc_start: 0.9077 (tpp) cc_final: 0.8310 (tpp) REVERT: A 466 MET cc_start: 0.9320 (mtt) cc_final: 0.8709 (mmt) REVERT: A 478 PHE cc_start: 0.9017 (m-10) cc_final: 0.8794 (m-10) REVERT: A 491 MET cc_start: 0.8860 (mtp) cc_final: 0.8410 (mtp) REVERT: A 495 LYS cc_start: 0.9742 (tttm) cc_final: 0.9499 (ttmm) REVERT: A 499 ILE cc_start: 0.9774 (mm) cc_final: 0.9568 (mt) REVERT: A 511 TYR cc_start: 0.9262 (m-80) cc_final: 0.8970 (m-80) REVERT: A 513 HIS cc_start: 0.9188 (m-70) cc_final: 0.8855 (m-70) REVERT: A 517 LEU cc_start: 0.9674 (mt) cc_final: 0.9412 (tp) REVERT: A 531 LYS cc_start: 0.9649 (tmtt) cc_final: 0.9298 (ptmm) REVERT: A 536 ASP cc_start: 0.9223 (m-30) cc_final: 0.8867 (p0) outliers start: 25 outliers final: 16 residues processed: 129 average time/residue: 0.0761 time to fit residues: 13.4132 Evaluate side-chains 125 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 734 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.3305 r_free = 0.3305 target = 0.067486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052553 restraints weight = 27253.622| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 5.84 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7123 Z= 0.172 Angle : 0.721 9.545 9783 Z= 0.385 Chirality : 0.047 0.198 1072 Planarity : 0.003 0.038 1097 Dihedral : 18.957 128.716 1277 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.89 % Allowed : 15.27 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.60 (0.30), residues: 743 helix: -0.59 (0.32), residues: 225 sheet: -2.14 (0.43), residues: 125 loop : -0.86 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 158 TYR 0.026 0.002 TYR A 306 PHE 0.030 0.002 PHE A 432 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 7123) covalent geometry : angle 0.72104 / 0.39 ( 9783) hydrogen bonds : bond 0.04402 / 2.84 ( 243) hydrogen bonds : angle 5.84871 / 4.03 ( 676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8668 (m-80) cc_final: 0.8240 (m-80) REVERT: A 30 LYS cc_start: 0.9639 (tmmt) cc_final: 0.9337 (tmmt) REVERT: A 51 MET cc_start: 0.9680 (mmt) cc_final: 0.8828 (tpp) REVERT: A 62 ILE cc_start: 0.8489 (mt) cc_final: 0.8271 (mt) REVERT: A 176 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9298 (mm) REVERT: A 191 MET cc_start: 0.9750 (mmm) cc_final: 0.9467 (mmm) REVERT: A 289 ASP cc_start: 0.8862 (t0) cc_final: 0.8359 (t0) REVERT: A 295 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8656 (pt0) REVERT: A 352 LEU cc_start: 0.9524 (mp) cc_final: 0.9116 (tp) REVERT: A 363 MET cc_start: 0.9072 (tpp) cc_final: 0.7906 (tpp) REVERT: A 478 PHE cc_start: 0.9016 (m-10) cc_final: 0.8811 (m-80) REVERT: A 491 MET cc_start: 0.8962 (mtp) cc_final: 0.8374 (mpp) REVERT: A 495 LYS cc_start: 0.9727 (tttm) cc_final: 0.9468 (ttmm) REVERT: A 511 TYR cc_start: 0.9315 (m-80) cc_final: 0.8987 (m-80) REVERT: A 513 HIS cc_start: 0.9190 (m-70) cc_final: 0.8690 (m-70) REVERT: A 531 LYS cc_start: 0.9650 (tmtt) cc_final: 0.9281 (ptmm) REVERT: A 533 MET cc_start: 0.8719 (tpt) cc_final: 0.8337 (tpt) REVERT: A 536 ASP cc_start: 0.9203 (m-30) cc_final: 0.8863 (p0) outliers start: 26 outliers final: 14 residues processed: 139 average time/residue: 0.0781 time to fit residues: 15.0972 Evaluate side-chains 127 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.0070 chunk 26 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051841 restraints weight = 27323.153| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.83 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7123 Z= 0.204 Angle : 0.743 9.947 9783 Z= 0.395 Chirality : 0.048 0.232 1072 Planarity : 0.003 0.029 1097 Dihedral : 18.843 128.247 1277 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.99 % Allowed : 17.81 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 743 helix: -0.46 (0.33), residues: 225 sheet: -2.17 (0.42), residues: 128 loop : -0.66 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 618 TYR 0.028 0.002 TYR A 306 PHE 0.016 0.002 PHE A 366 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 7123) covalent geometry : angle 0.74268 / 0.39 ( 9783) hydrogen bonds : bond 0.04387 / 2.82 ( 243) hydrogen bonds : angle 5.87408 / 4.03 ( 676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8651 (m-80) cc_final: 0.8224 (m-80) REVERT: A 51 MET cc_start: 0.9699 (mmt) cc_final: 0.8863 (tpp) REVERT: A 98 MET cc_start: 0.9405 (mmt) cc_final: 0.9148 (mmp) REVERT: A 176 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9305 (mm) REVERT: A 191 MET cc_start: 0.9774 (mmm) cc_final: 0.9496 (mmm) REVERT: A 289 ASP cc_start: 0.8897 (t0) cc_final: 0.8402 (t0) REVERT: A 302 MET cc_start: 0.8422 (mmm) cc_final: 0.7596 (mmm) REVERT: A 352 LEU cc_start: 0.9546 (mp) cc_final: 0.9134 (tp) REVERT: A 363 MET cc_start: 0.9124 (tpp) cc_final: 0.8012 (tpp) REVERT: A 478 PHE cc_start: 0.9126 (m-10) cc_final: 0.8827 (m-80) REVERT: A 491 MET cc_start: 0.8956 (mtp) cc_final: 0.8344 (mpp) REVERT: A 495 LYS cc_start: 0.9718 (tttm) cc_final: 0.9484 (ttmm) REVERT: A 513 HIS cc_start: 0.9241 (m-70) cc_final: 0.8594 (m-70) REVERT: A 536 ASP cc_start: 0.9258 (m-30) cc_final: 0.8903 (p0) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.0797 time to fit residues: 13.9519 Evaluate side-chains 123 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** 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 = 0.3281 r_free = 0.3281 target = 0.065703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050725 restraints weight = 28308.840| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 5.87 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7123 Z= 0.231 Angle : 0.746 9.977 9783 Z= 0.399 Chirality : 0.047 0.228 1072 Planarity : 0.004 0.047 1097 Dihedral : 18.807 128.041 1277 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.59 % Allowed : 18.26 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.31), residues: 743 helix: -0.28 (0.33), residues: 225 sheet: -1.99 (0.41), residues: 136 loop : -0.60 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.037 0.002 TYR A 306 PHE 0.019 0.002 PHE A 366 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 ( 7123) covalent geometry : angle 0.74644 / 0.40 ( 9783) hydrogen bonds : bond 0.04356 / 2.82 ( 243) hydrogen bonds : angle 5.86660 / 4.02 ( 676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8614 (m-80) cc_final: 0.8201 (m-80) REVERT: A 51 MET cc_start: 0.9693 (mmt) cc_final: 0.8860 (tpp) REVERT: A 98 MET cc_start: 0.9319 (mmt) cc_final: 0.8985 (mmp) REVERT: A 176 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9293 (mm) REVERT: A 191 MET cc_start: 0.9797 (mmm) cc_final: 0.9517 (mmm) REVERT: A 289 ASP cc_start: 0.8984 (t0) cc_final: 0.8520 (t0) REVERT: A 352 LEU cc_start: 0.9558 (mp) cc_final: 0.9156 (tp) REVERT: A 363 MET cc_start: 0.9146 (tpp) cc_final: 0.8231 (tpp) REVERT: A 478 PHE cc_start: 0.9178 (m-10) cc_final: 0.8784 (m-80) REVERT: A 491 MET cc_start: 0.8979 (mtp) cc_final: 0.8393 (mpp) REVERT: A 495 LYS cc_start: 0.9696 (tttm) cc_final: 0.9484 (ttmm) REVERT: A 513 HIS cc_start: 0.9283 (m-70) cc_final: 0.8643 (m-70) REVERT: A 531 LYS cc_start: 0.9661 (tmtt) cc_final: 0.9299 (tptp) REVERT: A 533 MET cc_start: 0.8736 (tpt) cc_final: 0.8455 (tpp) REVERT: A 536 ASP cc_start: 0.9243 (m-30) cc_final: 0.8898 (p0) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.0749 time to fit residues: 13.1629 Evaluate side-chains 120 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050875 restraints weight = 27276.849| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 5.74 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7123 Z= 0.201 Angle : 0.744 10.355 9783 Z= 0.391 Chirality : 0.048 0.258 1072 Planarity : 0.004 0.041 1097 Dihedral : 18.737 127.652 1277 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.44 % Allowed : 19.31 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.20 (0.31), residues: 743 helix: -0.19 (0.33), residues: 225 sheet: -1.81 (0.41), residues: 146 loop : -0.60 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.045 0.002 TYR A 306 PHE 0.017 0.002 PHE A 366 TRP 0.011 0.001 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 7123) covalent geometry : angle 0.74366 / 0.39 ( 9783) hydrogen bonds : bond 0.04203 / 2.70 ( 243) hydrogen bonds : angle 5.80142 / 3.98 ( 676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8627 (m-80) cc_final: 0.8233 (m-80) REVERT: A 51 MET cc_start: 0.9696 (mmt) cc_final: 0.8894 (tpp) REVERT: A 176 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9310 (mm) REVERT: A 191 MET cc_start: 0.9796 (mmm) cc_final: 0.9514 (mmm) REVERT: A 289 ASP cc_start: 0.8960 (t0) cc_final: 0.8458 (t0) REVERT: A 352 LEU cc_start: 0.9526 (mp) cc_final: 0.9104 (tp) REVERT: A 363 MET cc_start: 0.9170 (tpp) cc_final: 0.8137 (tpp) REVERT: A 478 PHE cc_start: 0.9204 (m-10) cc_final: 0.8874 (m-10) REVERT: A 491 MET cc_start: 0.8923 (mtp) cc_final: 0.8362 (mpp) REVERT: A 495 LYS cc_start: 0.9681 (tttm) cc_final: 0.9467 (ttmm) REVERT: A 513 HIS cc_start: 0.9325 (m-70) cc_final: 0.8605 (m-70) REVERT: A 531 LYS cc_start: 0.9656 (tmtt) cc_final: 0.9293 (tptp) REVERT: A 533 MET cc_start: 0.8659 (tpt) cc_final: 0.8448 (tpp) REVERT: A 536 ASP cc_start: 0.9264 (m-30) cc_final: 0.8908 (p0) outliers start: 23 outliers final: 19 residues processed: 128 average time/residue: 0.0767 time to fit residues: 13.6866 Evaluate side-chains 127 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 10.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.068344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053574 restraints weight = 28412.184| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 6.09 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7123 Z= 0.196 Angle : 0.755 16.607 9783 Z= 0.392 Chirality : 0.048 0.212 1072 Planarity : 0.004 0.049 1097 Dihedral : 18.687 127.304 1277 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.44 % Allowed : 20.06 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.08 (0.31), residues: 743 helix: -0.06 (0.34), residues: 225 sheet: -1.78 (0.41), residues: 146 loop : -0.53 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.044 0.002 TYR A 306 PHE 0.021 0.002 PHE A 366 TRP 0.010 0.001 TRP A 623 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 ( 7123) covalent geometry : angle 0.75480 / 0.39 ( 9783) hydrogen bonds : bond 0.04143 / 2.72 ( 243) hydrogen bonds : angle 5.78137 / 3.93 ( 676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8669 (m-80) cc_final: 0.8255 (m-80) REVERT: A 51 MET cc_start: 0.9712 (mmt) cc_final: 0.8938 (tpp) REVERT: A 176 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9322 (mm) REVERT: A 191 MET cc_start: 0.9791 (mmm) cc_final: 0.9491 (mmm) REVERT: A 289 ASP cc_start: 0.9000 (t0) cc_final: 0.8501 (t0) REVERT: A 363 MET cc_start: 0.9230 (tpp) cc_final: 0.8497 (mmm) REVERT: A 478 PHE cc_start: 0.9210 (m-10) cc_final: 0.8824 (m-10) REVERT: A 491 MET cc_start: 0.8838 (mtp) cc_final: 0.8419 (mtp) REVERT: A 495 LYS cc_start: 0.9677 (tttm) cc_final: 0.9466 (ttmm) REVERT: A 513 HIS cc_start: 0.9317 (m-70) cc_final: 0.8795 (m-70) REVERT: A 531 LYS cc_start: 0.9648 (tmtt) cc_final: 0.9379 (tppt) REVERT: A 533 MET cc_start: 0.8632 (tpt) cc_final: 0.8367 (tpp) REVERT: A 536 ASP cc_start: 0.9270 (m-30) cc_final: 0.8898 (p0) REVERT: A 646 LEU cc_start: 0.9424 (tt) cc_final: 0.9158 (tt) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.0774 time to fit residues: 13.7183 Evaluate side-chains 121 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049299 restraints weight = 29728.044| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 5.92 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7123 Z= 0.330 Angle : 0.825 12.219 9783 Z= 0.439 Chirality : 0.050 0.210 1072 Planarity : 0.004 0.053 1097 Dihedral : 18.741 127.533 1277 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.59 % Allowed : 21.56 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.34 (0.30), residues: 743 helix: -0.33 (0.32), residues: 225 sheet: -1.87 (0.40), residues: 155 loop : -0.63 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 667 TYR 0.042 0.002 TYR A 306 PHE 0.020 0.002 PHE A 366 TRP 0.009 0.002 TRP A 528 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.33 ( 7123) covalent geometry : angle 0.82459 / 0.44 ( 9783) hydrogen bonds : bond 0.04643 / 3.00 ( 243) hydrogen bonds : angle 5.96606 / 4.05 ( 676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8554 (m-80) cc_final: 0.8235 (m-80) REVERT: A 51 MET cc_start: 0.9707 (mmt) cc_final: 0.9035 (tpt) REVERT: A 169 MET cc_start: 0.9379 (mmm) cc_final: 0.9171 (mmm) REVERT: A 191 MET cc_start: 0.9785 (mmm) cc_final: 0.9522 (mmp) REVERT: A 289 ASP cc_start: 0.9025 (t0) cc_final: 0.8547 (t0) REVERT: A 363 MET cc_start: 0.9245 (tpp) cc_final: 0.8337 (tpp) REVERT: A 478 PHE cc_start: 0.9219 (m-10) cc_final: 0.8935 (m-10) REVERT: A 491 MET cc_start: 0.8962 (mtp) cc_final: 0.8454 (mpp) REVERT: A 495 LYS cc_start: 0.9696 (tttm) cc_final: 0.9484 (ttmm) REVERT: A 513 HIS cc_start: 0.9357 (m-70) cc_final: 0.8795 (m-70) REVERT: A 531 LYS cc_start: 0.9639 (tmtt) cc_final: 0.9307 (tptp) REVERT: A 533 MET cc_start: 0.8643 (tpt) cc_final: 0.8297 (tpp) REVERT: A 536 ASP cc_start: 0.9340 (m-30) cc_final: 0.8951 (p0) outliers start: 24 outliers final: 20 residues processed: 118 average time/residue: 0.0733 time to fit residues: 12.2651 Evaluate side-chains 116 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 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 = 0.3398 r_free = 0.3398 target = 0.067194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.051880 restraints weight = 27881.997| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 6.40 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7123 Z= 0.166 Angle : 0.788 16.423 9783 Z= 0.403 Chirality : 0.050 0.247 1072 Planarity : 0.004 0.053 1097 Dihedral : 18.680 127.612 1277 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.54 % Allowed : 22.75 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.11 (0.31), residues: 743 helix: -0.03 (0.34), residues: 222 sheet: -1.84 (0.40), residues: 150 loop : -0.54 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 263 TYR 0.040 0.002 TYR A 306 PHE 0.015 0.002 PHE A 366 TRP 0.005 0.001 TRP A 528 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 7123) covalent geometry : angle 0.78771 / 0.40 ( 9783) hydrogen bonds : bond 0.04201 / 2.75 ( 243) hydrogen bonds : angle 5.75220 / 3.94 ( 676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8619 (m-80) cc_final: 0.8228 (m-80) REVERT: A 51 MET cc_start: 0.9745 (mmt) cc_final: 0.9013 (tpp) REVERT: A 169 MET cc_start: 0.9364 (mmm) cc_final: 0.9157 (mmm) REVERT: A 191 MET cc_start: 0.9790 (mmm) cc_final: 0.9498 (mmm) REVERT: A 289 ASP cc_start: 0.8984 (t0) cc_final: 0.8486 (t0) REVERT: A 298 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8392 (tp40) REVERT: A 363 MET cc_start: 0.9211 (tpp) cc_final: 0.8429 (mmm) REVERT: A 478 PHE cc_start: 0.9156 (m-10) cc_final: 0.8806 (m-10) REVERT: A 491 MET cc_start: 0.8875 (mtp) cc_final: 0.8352 (mpp) REVERT: A 495 LYS cc_start: 0.9667 (tttm) cc_final: 0.9455 (ttmm) REVERT: A 513 HIS cc_start: 0.9269 (m-70) cc_final: 0.8889 (m-70) REVERT: A 531 LYS cc_start: 0.9642 (tmtt) cc_final: 0.9317 (tptp) REVERT: A 533 MET cc_start: 0.8626 (tpt) cc_final: 0.7954 (tpp) REVERT: A 536 ASP cc_start: 0.9320 (m-30) cc_final: 0.8957 (p0) REVERT: A 613 ARG cc_start: 0.9183 (ptt180) cc_final: 0.8267 (ptt90) REVERT: A 639 GLU cc_start: 0.7955 (tp30) cc_final: 0.7417 (mm-30) REVERT: A 705 GLN cc_start: 0.9694 (mt0) cc_final: 0.9434 (mt0) outliers start: 17 outliers final: 16 residues processed: 127 average time/residue: 0.0762 time to fit residues: 13.5805 Evaluate side-chains 117 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053141 restraints weight = 27875.611| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 6.21 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7123 Z= 0.164 Angle : 0.827 19.343 9783 Z= 0.420 Chirality : 0.049 0.223 1072 Planarity : 0.004 0.054 1097 Dihedral : 18.618 127.456 1277 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.10 % Allowed : 23.65 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.12 (0.31), residues: 743 helix: -0.21 (0.34), residues: 229 sheet: -1.69 (0.42), residues: 144 loop : -0.53 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.044 0.002 TYR A 306 PHE 0.014 0.002 PHE A 500 TRP 0.026 0.002 TRP A 482 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7123) covalent geometry : angle 0.82719 / 0.42 ( 9783) hydrogen bonds : bond 0.04214 / 2.89 ( 243) hydrogen bonds : angle 5.77306 / 3.97 ( 676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.44 seconds wall clock time: 24 minutes 50.40 seconds (1490.40 seconds total)