Starting phenix.real_space_refine on Tue Aug 4 21:24:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.map" model { file = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hio_34824/08_2026/8hio_34824.cif" } resolution = 3.73 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.211 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3952 2.51 5 N 1281 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 6681 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1019 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 15, 'rna3p': 31} Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4436 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 543} Chain breaks: 2 Chain: "D" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1224 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5151 SG CYS A 552 106.496 33.507 50.395 1.00185.32 S ATOM 5284 SG CYS A 569 106.415 36.312 50.252 1.00190.90 S ATOM 5302 SG CYS A 572 107.743 36.523 47.525 1.00196.84 S Time building chain proxies: 1.43, per 1000 atoms: 0.21 Number of scatterers: 6681 At special positions: 0 Unit cell: (118.101, 99.603, 102.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 47 15.00 Mg 1 11.99 O 1378 8.00 N 1281 7.00 C 3952 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: 0.48 Conformation dependent library (CDL) restraints added in 269.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " Number of angles added : 3 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 61.3% alpha, 12.2% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 92 through 119 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.501A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.575A pdb=" N ARG A 345 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.602A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.710A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.114A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.744A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'D' and resid 19 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 96 through 118 removed outlier: 3.640A pdb=" N ALA D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 145 removed outlier: 3.519A pdb=" N TYR D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 removed outlier: 3.598A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.716A pdb=" N THR A 299 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 281 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS A 297 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 283 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 295 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 285 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 293 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 287 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 11 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 5.947A pdb=" N ALA A 328 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 361 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.142A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 374 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.65 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: 1691 1.33 - 1.45: 1571 1.45 - 1.57: 3522 1.57 - 1.69: 93 1.69 - 1.81: 33 Bond restraints: 6910 Sorted by residual: bond pdb=" C TRP A 261 " pdb=" N ILE A 262 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.34e-02 5.57e+03 4.96e+00 bond pdb=" C ASP A 477 " pdb=" N GLN A 478 " ideal model delta sigma weight residual 1.332 1.311 0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CG LEU A 221 " pdb=" CD1 LEU A 221 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL A 194 " pdb=" CG1 VAL A 194 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB PHE A 443 " pdb=" CG PHE A 443 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.22e+00 ... (remaining 6905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9211 1.82 - 3.64: 314 3.64 - 5.46: 68 5.46 - 7.28: 6 7.28 - 9.10: 2 Bond angle restraints: 9601 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 113.12 108.77 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" O3' G B -11 " pdb=" C3' G B -11 " pdb=" C2' G B -11 " ideal model delta sigma weight residual 113.80 108.33 5.47 2.00e+00 2.50e-01 7.49e+00 angle pdb=" O3' A B -23 " pdb=" C3' A B -23 " pdb=" C2' A B -23 " ideal model delta sigma weight residual 113.80 108.36 5.44 2.00e+00 2.50e-01 7.39e+00 angle pdb=" CA LEU A 369 " pdb=" CB LEU A 369 " pdb=" CG LEU A 369 " ideal model delta sigma weight residual 116.30 107.20 9.10 3.50e+00 8.16e-02 6.75e+00 angle pdb=" C3' G B -8 " pdb=" C2' G B -8 " pdb=" O2' G B -8 " ideal model delta sigma weight residual 109.80 114.93 -5.13 2.00e+00 2.50e-01 6.57e+00 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 3392 15.15 - 30.30: 390 30.30 - 45.44: 151 45.44 - 60.59: 100 60.59 - 75.74: 27 Dihedral angle restraints: 4060 sinusoidal: 1968 harmonic: 2092 Sorted by residual: dihedral pdb=" C4' G B -11 " pdb=" C3' G B -11 " pdb=" C2' G B -11 " pdb=" C1' G B -11 " ideal model delta sinusoidal sigma weight residual 36.34 -37.99 74.34 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.35 -37.49 73.84 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' A B -23 " pdb=" C3' A B -23 " pdb=" C2' A B -23 " pdb=" C1' A B -23 " ideal model delta sinusoidal sigma weight residual 36.35 -37.08 73.43 1 3.10e+00 1.04e-01 7.14e+02 ... (remaining 4057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 901 0.059 - 0.118: 111 0.118 - 0.177: 8 0.177 - 0.236: 28 0.236 - 0.295: 48 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C2' G B -8 " pdb=" C3' G B -8 " pdb=" O2' G B -8 " pdb=" C1' G B -8 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" P U B -19 " pdb=" OP1 U B -19 " pdb=" OP2 U B -19 " pdb=" O5' U B -19 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' A B -30 " pdb=" C3' A B -30 " pdb=" O2' A B -30 " pdb=" C1' A B -30 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1093 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C GLN A 452 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 452 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 453 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 472 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ALA A 472 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 472 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 473 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 459 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS A 459 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 459 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 460 " 0.011 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 30 2.38 - 3.01: 3883 3.01 - 3.64: 10567 3.64 - 4.27: 15151 4.27 - 4.90: 24433 Nonbonded interactions: 54064 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 1.744 2.170 nonbonded pdb=" OP2 C B -21 " pdb="MG MG B 101 " model vdw 1.992 2.170 nonbonded pdb=" OP1 G B -7 " pdb=" NZ LYS A 14 " model vdw 2.111 3.120 nonbonded pdb=" OD2 ASP A 466 " pdb=" NE2 GLN A 470 " model vdw 2.147 3.120 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.153 3.040 ... (remaining 54059 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.020 Set scattering table: 0.020 Process input model: 8.140 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.006 0.056 6914 Z= 0.260 Angle : 0.990 36.858 9604 Z= 0.424 Chirality : 0.075 0.295 1096 Planarity : 0.004 0.031 1072 Dihedral : 18.281 75.740 2698 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.22 (0.32), residues: 707 helix: 2.70 (0.25), residues: 421 sheet: -0.24 (0.58), residues: 75 loop : -0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 205 TYR 0.019 0.002 TYR A 217 PHE 0.008 0.001 PHE A 443 TRP 0.022 0.002 TRP A 320 HIS 0.009 0.002 HIS A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 ( 6910) covalent geometry : angle 0.79953 / 0.40 ( 9601) hydrogen bonds : bond 0.17634 / 9.09 ( 402) hydrogen bonds : angle 5.92566 / 2.45 ( 1160) metal coordination : bond 0.03504 / 1.75 ( 4) metal coordination : angle 33.04508 / 11.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.237 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: symmetry clash REVERT: A 33 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 138 LYS cc_start: 0.8899 (tttt) cc_final: 0.8609 (tmtt) REVERT: A 169 ILE cc_start: 0.8917 (mm) cc_final: 0.8404 (tp) REVERT: A 333 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7792 (tpp80) REVERT: A 356 SER cc_start: 0.7773 (t) cc_final: 0.7542 (p) REVERT: A 420 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.5416 (mpp-170) REVERT: A 530 MET cc_start: 0.8056 (mmt) cc_final: 0.7513 (mmm) REVERT: D 27 LEU cc_start: 0.9226 (mt) cc_final: 0.8976 (mt) REVERT: D 32 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8005 (ttp-170) REVERT: D 42 TYR cc_start: 0.8057 (t80) cc_final: 0.7857 (t80) REVERT: D 46 LEU cc_start: 0.9019 (mt) cc_final: 0.8653 (mt) REVERT: D 50 TRP cc_start: 0.8448 (m100) cc_final: 0.8030 (m100) REVERT: D 98 ARG cc_start: 0.4191 (mtt180) cc_final: 0.3519 (tpm170) REVERT: D 115 ILE cc_start: 0.4875 (mt) cc_final: 0.4406 (mt) REVERT: D 127 LYS cc_start: 0.9577 (tppt) cc_final: 0.9344 (tptp) REVERT: D 163 LYS cc_start: 0.8615 (mttt) cc_final: 0.8395 (mmtt) REVERT: D 185 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7354 (mtp180) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1301 time to fit residues: 29.4757 Evaluate side-chains 121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 516 HIS D 30 ASN D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.177081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.139463 restraints weight = 14589.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.143981 restraints weight = 7452.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.146948 restraints weight = 4971.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.148816 restraints weight = 3855.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.149816 restraints weight = 3282.510| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6914 Z= 0.225 Angle : 1.030 15.036 9604 Z= 0.455 Chirality : 0.081 0.686 1096 Planarity : 0.005 0.055 1072 Dihedral : 17.279 161.937 1364 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.27 % Allowed : 18.59 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.42 (0.33), residues: 707 helix: 2.77 (0.24), residues: 426 sheet: 0.05 (0.62), residues: 73 loop : -0.32 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 103 TYR 0.019 0.002 TYR A 217 PHE 0.007 0.001 PHE A 582 TRP 0.018 0.002 TRP A 450 HIS 0.011 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 ( 6910) covalent geometry : angle 1.02059 / 0.45 ( 9601) hydrogen bonds : bond 0.05122 / 2.69 ( 402) hydrogen bonds : angle 4.48243 / 1.81 ( 1160) metal coordination : bond 0.02074 / 1.04 ( 4) metal coordination : angle 7.74939 / 2.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.235 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 9 MET cc_start: 0.8146 (mtt) cc_final: 0.7852 (mtm) REVERT: A 127 LYS cc_start: 0.9265 (tmmt) cc_final: 0.9059 (tmmt) REVERT: A 169 ILE cc_start: 0.8654 (mm) cc_final: 0.8054 (tp) REVERT: A 185 ARG cc_start: 0.6652 (ttp-170) cc_final: 0.6332 (mtm180) REVERT: A 356 SER cc_start: 0.7511 (t) cc_final: 0.7263 (p) REVERT: A 420 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.5411 (mpp-170) REVERT: D 23 GLN cc_start: 0.8822 (tp40) cc_final: 0.8576 (mt0) REVERT: D 32 ARG cc_start: 0.8566 (ttp80) cc_final: 0.7981 (ttp-170) REVERT: D 42 TYR cc_start: 0.8180 (t80) cc_final: 0.7873 (t80) REVERT: D 46 LEU cc_start: 0.9192 (mt) cc_final: 0.8737 (mm) REVERT: D 50 TRP cc_start: 0.8163 (m100) cc_final: 0.7904 (m100) REVERT: D 138 LYS cc_start: 0.9368 (mttt) cc_final: 0.9111 (mttp) REVERT: D 167 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8132 (mmmt) REVERT: D 185 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7375 (mtm180) outliers start: 19 outliers final: 7 residues processed: 136 average time/residue: 0.1107 time to fit residues: 18.7178 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 419 GLN A 516 HIS D 29 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN D 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.169679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133540 restraints weight = 14892.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.137661 restraints weight = 8067.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.140400 restraints weight = 5523.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.142027 restraints weight = 4343.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.142916 restraints weight = 3752.196| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6914 Z= 0.221 Angle : 0.866 12.273 9604 Z= 0.395 Chirality : 0.068 0.612 1096 Planarity : 0.005 0.050 1072 Dihedral : 17.462 166.900 1364 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.30 % Allowed : 18.76 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.28 (0.33), residues: 707 helix: 2.66 (0.24), residues: 425 sheet: -0.04 (0.61), residues: 77 loop : -0.35 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.019 0.002 TYR A 217 PHE 0.007 0.001 PHE A 155 TRP 0.035 0.002 TRP A 26 HIS 0.010 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 6910) covalent geometry : angle 0.86498 / 0.39 ( 9601) hydrogen bonds : bond 0.04788 / 2.50 ( 402) hydrogen bonds : angle 4.39823 / 1.77 ( 1160) metal coordination : bond 0.01807 / 0.90 ( 4) metal coordination : angle 2.75020 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.233 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: A 9 MET cc_start: 0.8172 (mtt) cc_final: 0.7857 (mtm) REVERT: A 29 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7505 (t-90) REVERT: A 63 MET cc_start: 0.8934 (ptp) cc_final: 0.8342 (ptp) REVERT: A 127 LYS cc_start: 0.9308 (tmmt) cc_final: 0.9025 (tmmt) REVERT: A 356 SER cc_start: 0.7549 (t) cc_final: 0.7272 (p) REVERT: A 530 MET cc_start: 0.7629 (mmp) cc_final: 0.7420 (mmp) REVERT: D 42 TYR cc_start: 0.8168 (t80) cc_final: 0.7940 (t80) REVERT: D 50 TRP cc_start: 0.8322 (m100) cc_final: 0.8122 (m100) REVERT: D 167 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8221 (mmmt) REVERT: D 185 ARG cc_start: 0.8317 (mmm160) cc_final: 0.7372 (mtm180) outliers start: 25 outliers final: 14 residues processed: 127 average time/residue: 0.0882 time to fit residues: 14.8753 Evaluate side-chains 109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN A 452 GLN D 29 HIS D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.166272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126289 restraints weight = 14060.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.130464 restraints weight = 7419.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.133285 restraints weight = 5066.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134790 restraints weight = 3979.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.135985 restraints weight = 3465.751| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6914 Z= 0.286 Angle : 0.933 13.024 9604 Z= 0.428 Chirality : 0.070 0.572 1096 Planarity : 0.005 0.041 1072 Dihedral : 17.586 174.685 1364 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.68 % Allowed : 21.86 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.00 (0.32), residues: 707 helix: 2.53 (0.24), residues: 425 sheet: -0.28 (0.64), residues: 71 loop : -0.63 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.019 0.002 TYR A 217 PHE 0.007 0.001 PHE A 155 TRP 0.025 0.002 TRP A 450 HIS 0.015 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.29 ( 6910) covalent geometry : angle 0.93189 / 0.43 ( 9601) hydrogen bonds : bond 0.05150 / 2.69 ( 402) hydrogen bonds : angle 4.65394 / 1.87 ( 1160) metal coordination : bond 0.01701 / 0.85 ( 4) metal coordination : angle 2.93319 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.201 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 9 MET cc_start: 0.8308 (mtt) cc_final: 0.7924 (mtm) REVERT: A 29 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7434 (t-90) REVERT: A 63 MET cc_start: 0.9135 (ptp) cc_final: 0.8492 (ptp) REVERT: A 93 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5963 (tp) REVERT: A 127 LYS cc_start: 0.9386 (tmmt) cc_final: 0.9054 (tmmt) REVERT: A 356 SER cc_start: 0.7524 (t) cc_final: 0.7196 (p) REVERT: A 478 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: D 23 GLN cc_start: 0.8949 (tp40) cc_final: 0.8521 (pt0) REVERT: D 24 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8287 (mm-40) REVERT: D 32 ARG cc_start: 0.8499 (ttp80) cc_final: 0.7970 (ttm170) REVERT: D 50 TRP cc_start: 0.8346 (m100) cc_final: 0.8067 (m100) REVERT: D 127 LYS cc_start: 0.9423 (tppt) cc_final: 0.9013 (tppt) REVERT: D 167 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8278 (mmmt) REVERT: D 181 LEU cc_start: 0.7953 (tp) cc_final: 0.7354 (pp) REVERT: D 184 HIS cc_start: 0.6122 (m-70) cc_final: 0.5839 (m90) REVERT: D 185 ARG cc_start: 0.8512 (mmm160) cc_final: 0.7399 (mtm180) outliers start: 33 outliers final: 21 residues processed: 124 average time/residue: 0.0946 time to fit residues: 15.1779 Evaluate side-chains 119 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.165260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126907 restraints weight = 14528.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.131123 restraints weight = 7602.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133745 restraints weight = 5098.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135472 restraints weight = 3989.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136363 restraints weight = 3415.319| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6914 Z= 0.274 Angle : 0.928 13.056 9604 Z= 0.424 Chirality : 0.069 0.533 1096 Planarity : 0.005 0.039 1072 Dihedral : 17.639 177.466 1364 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.51 % Allowed : 23.41 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.70 (0.32), residues: 707 helix: 2.31 (0.24), residues: 425 sheet: -0.65 (0.63), residues: 71 loop : -0.71 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.030 0.003 TYR D 42 PHE 0.010 0.002 PHE A 443 TRP 0.020 0.002 TRP A 450 HIS 0.015 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 ( 6910) covalent geometry : angle 0.92651 / 0.42 ( 9601) hydrogen bonds : bond 0.05076 / 2.64 ( 402) hydrogen bonds : angle 4.64262 / 1.88 ( 1160) metal coordination : bond 0.01289 / 0.64 ( 4) metal coordination : angle 2.83250 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.239 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 9 MET cc_start: 0.8269 (mtt) cc_final: 0.7827 (mtm) REVERT: A 29 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7393 (t-90) REVERT: A 127 LYS cc_start: 0.9419 (tmmt) cc_final: 0.9135 (tmmt) REVERT: A 299 THR cc_start: 0.7934 (m) cc_final: 0.7375 (p) REVERT: A 475 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7088 (mm) REVERT: D 23 GLN cc_start: 0.8963 (tp40) cc_final: 0.8519 (pt0) REVERT: D 32 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8119 (ttm-80) REVERT: D 50 TRP cc_start: 0.8353 (m100) cc_final: 0.8085 (m100) REVERT: D 137 GLN cc_start: 0.9092 (mt0) cc_final: 0.8822 (mm110) REVERT: D 138 LYS cc_start: 0.9232 (ptpt) cc_final: 0.8967 (ptpp) REVERT: D 184 HIS cc_start: 0.6324 (m-70) cc_final: 0.5901 (m90) REVERT: D 185 ARG cc_start: 0.8677 (mmm160) cc_final: 0.7392 (mtm180) outliers start: 32 outliers final: 20 residues processed: 119 average time/residue: 0.0950 time to fit residues: 14.7364 Evaluate side-chains 113 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 40.0000 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.167451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127864 restraints weight = 14117.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132241 restraints weight = 7459.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135089 restraints weight = 5033.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.136666 restraints weight = 3938.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.137940 restraints weight = 3405.628| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6914 Z= 0.188 Angle : 0.832 11.170 9604 Z= 0.384 Chirality : 0.064 0.475 1096 Planarity : 0.004 0.038 1072 Dihedral : 17.507 177.801 1364 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.65 % Allowed : 24.61 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.87 (0.32), residues: 707 helix: 2.43 (0.24), residues: 425 sheet: -0.70 (0.69), residues: 61 loop : -0.57 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 379 TYR 0.015 0.002 TYR D 141 PHE 0.007 0.001 PHE A 582 TRP 0.035 0.002 TRP A 450 HIS 0.014 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 6910) covalent geometry : angle 0.83116 / 0.38 ( 9601) hydrogen bonds : bond 0.04380 / 2.28 ( 402) hydrogen bonds : angle 4.39014 / 1.78 ( 1160) metal coordination : bond 0.01127 / 0.56 ( 4) metal coordination : angle 2.25967 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8161 (mtt) cc_final: 0.7730 (mtm) REVERT: A 29 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7310 (t-90) REVERT: A 127 LYS cc_start: 0.9388 (tmmt) cc_final: 0.9054 (tmmt) REVERT: A 138 LYS cc_start: 0.8532 (tptt) cc_final: 0.8265 (tptp) REVERT: A 299 THR cc_start: 0.7947 (m) cc_final: 0.7445 (p) REVERT: A 475 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7029 (mm) REVERT: A 556 ASN cc_start: 0.8580 (m-40) cc_final: 0.7982 (m110) REVERT: D 23 GLN cc_start: 0.8812 (tp40) cc_final: 0.8591 (pt0) REVERT: D 32 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8096 (ttm-80) REVERT: D 42 TYR cc_start: 0.8161 (t80) cc_final: 0.7860 (t80) REVERT: D 50 TRP cc_start: 0.8279 (m100) cc_final: 0.8055 (m100) REVERT: D 184 HIS cc_start: 0.6323 (m-70) cc_final: 0.5864 (m90) REVERT: D 185 ARG cc_start: 0.8661 (mmm160) cc_final: 0.7383 (mtm180) outliers start: 27 outliers final: 17 residues processed: 117 average time/residue: 0.0960 time to fit residues: 14.5883 Evaluate side-chains 108 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 GLN D 29 HIS D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.131266 restraints weight = 13979.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135506 restraints weight = 7317.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.138287 restraints weight = 4918.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.139777 restraints weight = 3826.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.141045 restraints weight = 3315.336| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6914 Z= 0.151 Angle : 0.794 10.970 9604 Z= 0.369 Chirality : 0.061 0.456 1096 Planarity : 0.004 0.039 1072 Dihedral : 17.405 177.288 1364 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.48 % Allowed : 25.13 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.97 (0.33), residues: 707 helix: 2.44 (0.25), residues: 426 sheet: -0.63 (0.68), residues: 61 loop : -0.40 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.011 0.001 TYR A 217 PHE 0.009 0.001 PHE A 545 TRP 0.025 0.002 TRP A 450 HIS 0.014 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6910) covalent geometry : angle 0.79346 / 0.37 ( 9601) hydrogen bonds : bond 0.03975 / 2.06 ( 402) hydrogen bonds : angle 4.21356 / 1.71 ( 1160) metal coordination : bond 0.00616 / 0.31 ( 4) metal coordination : angle 1.67778 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.233 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 9 MET cc_start: 0.7812 (mtt) cc_final: 0.7456 (mtm) REVERT: A 29 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7270 (t-90) REVERT: A 127 LYS cc_start: 0.9388 (tmmt) cc_final: 0.9059 (tmmt) REVERT: A 138 LYS cc_start: 0.8537 (tptt) cc_final: 0.8205 (tptp) REVERT: A 194 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7341 (p) REVERT: A 299 THR cc_start: 0.7775 (m) cc_final: 0.7296 (p) REVERT: A 475 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6892 (mm) REVERT: A 556 ASN cc_start: 0.8499 (m-40) cc_final: 0.8036 (m110) REVERT: D 23 GLN cc_start: 0.8986 (tp40) cc_final: 0.8584 (pt0) REVERT: D 32 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8113 (ttm-80) REVERT: D 42 TYR cc_start: 0.8244 (t80) cc_final: 0.7859 (t80) REVERT: D 46 LEU cc_start: 0.8984 (mp) cc_final: 0.8234 (tp) REVERT: D 50 TRP cc_start: 0.8211 (m100) cc_final: 0.7919 (m100) REVERT: D 184 HIS cc_start: 0.6266 (m-70) cc_final: 0.5812 (m90) REVERT: D 185 ARG cc_start: 0.8621 (mmm160) cc_final: 0.7407 (mtm180) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.0915 time to fit residues: 13.4290 Evaluate side-chains 109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 132 GLN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.166354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127713 restraints weight = 14073.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.131811 restraints weight = 7494.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.134543 restraints weight = 5090.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136284 restraints weight = 3992.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137170 restraints weight = 3419.308| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6914 Z= 0.234 Angle : 0.881 11.841 9604 Z= 0.407 Chirality : 0.066 0.500 1096 Planarity : 0.005 0.037 1072 Dihedral : 17.486 177.575 1364 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.96 % Allowed : 25.47 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.69 (0.33), residues: 707 helix: 2.26 (0.25), residues: 425 sheet: -0.88 (0.62), residues: 71 loop : -0.50 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 205 TYR 0.018 0.002 TYR A 217 PHE 0.007 0.002 PHE A 443 TRP 0.045 0.002 TRP A 50 HIS 0.013 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 ( 6910) covalent geometry : angle 0.88014 / 0.41 ( 9601) hydrogen bonds : bond 0.04635 / 2.40 ( 402) hydrogen bonds : angle 4.51449 / 1.83 ( 1160) metal coordination : bond 0.00890 / 0.45 ( 4) metal coordination : angle 2.41346 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8022 (mtt) cc_final: 0.7589 (mtm) REVERT: A 29 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7371 (t-90) REVERT: A 127 LYS cc_start: 0.9412 (tmmt) cc_final: 0.9074 (tmmt) REVERT: A 299 THR cc_start: 0.7801 (m) cc_final: 0.7310 (p) REVERT: A 475 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6995 (mm) REVERT: A 556 ASN cc_start: 0.8580 (m110) cc_final: 0.8021 (m110) REVERT: D 23 GLN cc_start: 0.8982 (tp40) cc_final: 0.8574 (pt0) REVERT: D 32 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8157 (ttm-80) REVERT: D 42 TYR cc_start: 0.8222 (t80) cc_final: 0.8021 (t80) REVERT: D 50 TRP cc_start: 0.8273 (m100) cc_final: 0.8073 (m100) REVERT: D 184 HIS cc_start: 0.6374 (m-70) cc_final: 0.6125 (m-70) REVERT: D 185 ARG cc_start: 0.8708 (mmm160) cc_final: 0.7383 (mtm180) outliers start: 23 outliers final: 18 residues processed: 107 average time/residue: 0.0927 time to fit residues: 12.9782 Evaluate side-chains 109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.128442 restraints weight = 14186.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.132729 restraints weight = 7520.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135346 restraints weight = 5069.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137222 restraints weight = 3992.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138162 restraints weight = 3407.159| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6914 Z= 0.197 Angle : 0.846 10.735 9604 Z= 0.389 Chirality : 0.064 0.496 1096 Planarity : 0.004 0.037 1072 Dihedral : 17.421 178.626 1364 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.96 % Allowed : 25.47 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.72 (0.33), residues: 707 helix: 2.28 (0.25), residues: 425 sheet: -0.86 (0.62), residues: 71 loop : -0.49 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 173 TYR 0.016 0.002 TYR A 217 PHE 0.008 0.001 PHE A 582 TRP 0.023 0.002 TRP A 450 HIS 0.013 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 6910) covalent geometry : angle 0.84472 / 0.39 ( 9601) hydrogen bonds : bond 0.04314 / 2.24 ( 402) hydrogen bonds : angle 4.41966 / 1.79 ( 1160) metal coordination : bond 0.00813 / 0.41 ( 4) metal coordination : angle 2.27601 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 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: A 9 MET cc_start: 0.8000 (mtt) cc_final: 0.7575 (mtm) REVERT: A 26 TRP cc_start: 0.8079 (t60) cc_final: 0.6747 (t60) REVERT: A 29 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7334 (t-90) REVERT: A 50 TRP cc_start: 0.7376 (m100) cc_final: 0.7166 (m100) REVERT: A 127 LYS cc_start: 0.9413 (tmmt) cc_final: 0.9076 (tmmt) REVERT: A 138 LYS cc_start: 0.8480 (tptt) cc_final: 0.8108 (tptp) REVERT: A 299 THR cc_start: 0.7949 (m) cc_final: 0.7452 (p) REVERT: A 475 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7025 (mm) REVERT: A 556 ASN cc_start: 0.8609 (m110) cc_final: 0.8002 (m110) REVERT: D 23 GLN cc_start: 0.8904 (tp40) cc_final: 0.8567 (pt0) REVERT: D 32 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8177 (ttm-80) REVERT: D 42 TYR cc_start: 0.8021 (t80) cc_final: 0.7689 (t80) REVERT: D 46 LEU cc_start: 0.8951 (mp) cc_final: 0.8334 (tp) REVERT: D 50 TRP cc_start: 0.8239 (m100) cc_final: 0.7980 (m100) REVERT: D 184 HIS cc_start: 0.6398 (m-70) cc_final: 0.6148 (m-70) REVERT: D 185 ARG cc_start: 0.8725 (mmm160) cc_final: 0.7395 (mtm180) outliers start: 23 outliers final: 17 residues processed: 104 average time/residue: 0.0883 time to fit residues: 12.0656 Evaluate side-chains 104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.171551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.132738 restraints weight = 14154.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136984 restraints weight = 7436.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.139817 restraints weight = 5016.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141569 restraints weight = 3910.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142553 restraints weight = 3344.317| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6914 Z= 0.144 Angle : 0.803 18.696 9604 Z= 0.365 Chirality : 0.059 0.463 1096 Planarity : 0.004 0.040 1072 Dihedral : 17.270 179.421 1364 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.58 % Allowed : 27.02 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.02 (0.33), residues: 707 helix: 2.46 (0.25), residues: 426 sheet: -0.59 (0.62), residues: 72 loop : -0.29 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.012 0.001 TYR D 141 PHE 0.007 0.001 PHE A 582 TRP 0.018 0.002 TRP A 450 HIS 0.012 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6910) covalent geometry : angle 0.80276 / 0.36 ( 9601) hydrogen bonds : bond 0.03818 / 1.98 ( 402) hydrogen bonds : angle 4.24548 / 1.71 ( 1160) metal coordination : bond 0.00403 / 0.20 ( 4) metal coordination : angle 1.67256 / 0.56 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.205 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 26 TRP cc_start: 0.8019 (t60) cc_final: 0.6742 (t60) REVERT: A 29 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7180 (t-90) REVERT: A 63 MET cc_start: 0.9129 (ppp) cc_final: 0.8639 (pmm) REVERT: A 127 LYS cc_start: 0.9404 (tmmt) cc_final: 0.9059 (tmmt) REVERT: A 138 LYS cc_start: 0.8563 (tptt) cc_final: 0.8201 (tptp) REVERT: A 299 THR cc_start: 0.7795 (m) cc_final: 0.7308 (p) REVERT: A 475 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6843 (mm) REVERT: A 556 ASN cc_start: 0.8571 (m110) cc_final: 0.7990 (m110) REVERT: A 568 ARG cc_start: 0.7706 (tpp80) cc_final: 0.6937 (tpp80) REVERT: A 575 MET cc_start: 0.8191 (tpp) cc_final: 0.7832 (tpp) REVERT: D 23 GLN cc_start: 0.9005 (tp40) cc_final: 0.8582 (pt0) REVERT: D 32 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8140 (ttm-80) REVERT: D 42 TYR cc_start: 0.7981 (t80) cc_final: 0.7702 (t80) REVERT: D 46 LEU cc_start: 0.8977 (mp) cc_final: 0.8468 (tp) REVERT: D 184 HIS cc_start: 0.6302 (m-70) cc_final: 0.6066 (m-70) REVERT: D 185 ARG cc_start: 0.8658 (mmm160) cc_final: 0.7348 (mtp180) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.0967 time to fit residues: 12.5592 Evaluate side-chains 100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.0170 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 HIS D 29 HIS D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.171196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132316 restraints weight = 14011.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136496 restraints weight = 7462.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139167 restraints weight = 5046.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141062 restraints weight = 3969.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142023 restraints weight = 3377.382| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6914 Z= 0.153 Angle : 0.813 17.271 9604 Z= 0.372 Chirality : 0.059 0.468 1096 Planarity : 0.004 0.040 1072 Dihedral : 17.222 179.445 1364 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.10 % Allowed : 26.51 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.84 (0.33), residues: 707 helix: 2.27 (0.25), residues: 432 sheet: -0.42 (0.63), residues: 72 loop : -0.44 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.012 0.001 TYR D 42 PHE 0.005 0.001 PHE A 582 TRP 0.046 0.002 TRP A 50 HIS 0.012 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6910) covalent geometry : angle 0.81242 / 0.37 ( 9601) hydrogen bonds : bond 0.03900 / 2.03 ( 402) hydrogen bonds : angle 4.27557 / 1.73 ( 1160) metal coordination : bond 0.00438 / 0.22 ( 4) metal coordination : angle 1.67260 / 0.56 ( 3) =============================================================================== Job complete usr+sys time: 1439.04 seconds wall clock time: 25 minutes 30.18 seconds (1530.18 seconds total)