Starting phenix.real_space_refine on Thu Jul 2 05:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hio_34824/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hio_34824/07_2026/8hio_34824.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 1.65, per 1000 atoms: 0.25 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: 0.61 Conformation dependent library (CDL) restraints added in 373.6 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: 0.50 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: 1.14 Time building geometry restraints manager: 0.83 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: 9367 1.82 - 3.64: 205 3.64 - 5.46: 23 5.46 - 7.28: 4 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=" 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=" C LEU A 318 " pdb=" N GLY A 319 " pdb=" CA GLY A 319 " ideal model delta sigma weight residual 120.51 124.36 -3.85 1.63e+00 3.76e-01 5.57e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 122.42 118.79 3.63 1.55e+00 4.16e-01 5.48e+00 angle pdb=" C ALA A 281 " pdb=" N GLU A 282 " pdb=" CA GLU A 282 " ideal model delta sigma weight residual 122.99 119.73 3.26 1.41e+00 5.03e-01 5.34e+00 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.19: 3648 19.19 - 38.38: 294 38.38 - 57.58: 101 57.58 - 76.77: 13 76.77 - 95.96: 4 Dihedral angle restraints: 4060 sinusoidal: 1968 harmonic: 2092 Sorted by residual: dihedral pdb=" O4' U B 6 " pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sinusoidal sigma weight residual -160.00 -83.79 -76.21 1 1.50e+01 4.44e-03 3.25e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -171.33 65.33 1 1.70e+01 3.46e-03 1.94e+01 dihedral pdb=" O4' C B 15 " pdb=" C1' C B 15 " pdb=" N1 C B 15 " pdb=" C2 C B 15 " ideal model delta sinusoidal sigma weight residual -160.00 -104.45 -55.55 1 1.50e+01 4.44e-03 1.85e+01 ... (remaining 4057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 688 0.029 - 0.058: 282 0.058 - 0.087: 86 0.087 - 0.115: 30 0.115 - 0.144: 10 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL A 268 " pdb=" N VAL A 268 " pdb=" C VAL A 268 " pdb=" CB VAL A 268 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- 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 : 0.005 0.056 6914 Z= 0.255 Angle : 0.884 36.858 9604 Z= 0.391 Chirality : 0.037 0.144 1096 Planarity : 0.004 0.031 1072 Dihedral : 15.537 95.962 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 0.00531 / 0.25 ( 6910) covalent geometry : angle 0.66388 / 0.36 ( 9601) hydrogen bonds : bond 0.17634 / 10.20 ( 402) hydrogen bonds : angle 5.92566 / 3.44 ( 1160) metal coordination : bond 0.03504 / 1.81 ( 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 : 0.150 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: 0.1182 time to fit residues: 26.7022 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 : 0.158 ------------------------------------------------------------------------------- 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 A 449 GLN A 516 HIS D 30 ASN D 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.170865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.134381 restraints weight = 15316.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.138620 restraints weight = 8166.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.141295 restraints weight = 5556.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143003 restraints weight = 4370.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.143884 restraints weight = 3761.279| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6914 Z= 0.185 Angle : 0.645 11.223 9604 Z= 0.336 Chirality : 0.039 0.166 1096 Planarity : 0.005 0.059 1072 Dihedral : 12.476 97.277 1364 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.10 % Allowed : 18.59 % Favored : 78.31 % 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: 2.74 (0.25), residues: 427 sheet: 0.07 (0.62), residues: 73 loop : -0.28 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 0.012 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6910) covalent geometry : angle 0.63440 / 0.33 ( 9601) hydrogen bonds : bond 0.05016 / 2.97 ( 402) hydrogen bonds : angle 4.43179 / 2.61 ( 1160) metal coordination : bond 0.02670 / 1.36 ( 4) metal coordination : angle 6.59503 / 2.20 ( 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: 18 poor density : 126 time to evaluate : 0.219 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: A 9 MET cc_start: 0.8088 (mtt) cc_final: 0.7817 (mtm) REVERT: A 93 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6399 (tp) REVERT: A 127 LYS cc_start: 0.9268 (tmmt) cc_final: 0.9052 (tmmt) REVERT: A 169 ILE cc_start: 0.8634 (mm) cc_final: 0.8043 (tp) REVERT: A 356 SER cc_start: 0.7449 (t) cc_final: 0.7228 (p) REVERT: A 420 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.5460 (mpp-170) REVERT: D 23 GLN cc_start: 0.8842 (tp40) cc_final: 0.8568 (mt0) REVERT: D 32 ARG cc_start: 0.8468 (ttp80) cc_final: 0.7897 (ttp-170) REVERT: D 42 TYR cc_start: 0.8167 (t80) cc_final: 0.7872 (t80) REVERT: D 46 LEU cc_start: 0.9176 (mt) cc_final: 0.8723 (mm) REVERT: D 50 TRP cc_start: 0.8177 (m100) cc_final: 0.7946 (m100) REVERT: D 138 LYS cc_start: 0.9402 (mttt) cc_final: 0.9146 (mttp) REVERT: D 154 SER cc_start: 0.7709 (m) cc_final: 0.7505 (p) REVERT: D 167 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8123 (mmmt) REVERT: D 185 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7388 (mtm180) outliers start: 18 outliers final: 7 residues processed: 136 average time/residue: 0.0960 time to fit residues: 16.2476 Evaluate side-chains 114 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 93 LEU 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: 20.0000 chunk 72 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 267 GLN A 516 HIS D 29 HIS 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 = 0.4452 r_free = 0.4452 target = 0.173994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.135505 restraints weight = 14478.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.139992 restraints weight = 7504.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.142938 restraints weight = 5012.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.144719 restraints weight = 3896.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.145618 restraints weight = 3331.710| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3221 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= 0.213 Angle : 0.640 7.749 9604 Z= 0.331 Chirality : 0.039 0.220 1096 Planarity : 0.005 0.049 1072 Dihedral : 12.579 97.920 1364 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.79 % Allowed : 19.62 % Favored : 76.59 % 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: 2.26 (0.33), residues: 707 helix: 2.64 (0.25), residues: 425 sheet: -0.04 (0.61), residues: 77 loop : -0.37 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 146 TYR 0.020 0.002 TYR A 217 PHE 0.008 0.001 PHE A 155 TRP 0.026 0.002 TRP A 450 HIS 0.011 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 ( 6910) covalent geometry : angle 0.63862 / 0.33 ( 9601) hydrogen bonds : bond 0.04893 / 2.90 ( 402) hydrogen bonds : angle 4.40371 / 2.63 ( 1160) metal coordination : bond 0.01631 / 0.82 ( 4) metal coordination : angle 2.67432 / 0.89 ( 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 132 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8219 (mtt) cc_final: 0.7918 (mtm) REVERT: A 29 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7466 (t-90) REVERT: A 63 MET cc_start: 0.8990 (ptp) cc_final: 0.8393 (ptp) REVERT: A 127 LYS cc_start: 0.9332 (tmmt) cc_final: 0.9047 (tmmt) REVERT: A 185 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6939 (mtm180) REVERT: A 356 SER cc_start: 0.7668 (t) cc_final: 0.7348 (p) REVERT: D 24 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8304 (mm-40) REVERT: D 42 TYR cc_start: 0.8155 (t80) cc_final: 0.7951 (t80) REVERT: D 127 LYS cc_start: 0.9427 (tppt) cc_final: 0.9027 (tppt) REVERT: D 167 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8215 (mmmt) REVERT: D 181 LEU cc_start: 0.7754 (tp) cc_final: 0.7508 (pp) REVERT: D 185 ARG cc_start: 0.8343 (mmm160) cc_final: 0.7380 (mtm180) outliers start: 22 outliers final: 12 residues processed: 123 average time/residue: 0.0815 time to fit residues: 13.0710 Evaluate side-chains 111 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 185 ARG 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 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 50.0000 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 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 = 0.4378 r_free = 0.4378 target = 0.167245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128613 restraints weight = 14052.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132806 restraints weight = 7289.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.135624 restraints weight = 4892.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137343 restraints weight = 3806.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138412 restraints weight = 3257.955| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6914 Z= 0.215 Angle : 0.647 8.097 9604 Z= 0.337 Chirality : 0.038 0.162 1096 Planarity : 0.004 0.041 1072 Dihedral : 12.594 98.439 1364 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.99 % Allowed : 21.69 % Favored : 73.32 % 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: 2.24 (0.33), residues: 707 helix: 2.68 (0.25), residues: 425 sheet: 0.13 (0.73), residues: 61 loop : -0.54 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 379 TYR 0.018 0.002 TYR A 217 PHE 0.006 0.001 PHE A 155 TRP 0.027 0.002 TRP A 450 HIS 0.015 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 ( 6910) covalent geometry : angle 0.64515 / 0.34 ( 9601) hydrogen bonds : bond 0.04755 / 2.82 ( 402) hydrogen bonds : angle 4.49286 / 2.70 ( 1160) metal coordination : bond 0.01452 / 0.73 ( 4) metal coordination : angle 2.71250 / 0.90 ( 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 130 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.210 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: 0.8189 (mtt) cc_final: 0.7870 (mtm) REVERT: A 26 TRP cc_start: 0.8358 (t60) cc_final: 0.6978 (t60) REVERT: A 29 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: A 63 MET cc_start: 0.9088 (ptp) cc_final: 0.8511 (ptp) REVERT: A 127 LYS cc_start: 0.9381 (tmmt) cc_final: 0.9038 (tmmt) REVERT: A 185 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7016 (mtm180) REVERT: A 187 ASP cc_start: 0.8865 (p0) cc_final: 0.8602 (p0) REVERT: A 356 SER cc_start: 0.7601 (t) cc_final: 0.7302 (p) REVERT: A 475 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7006 (mm) REVERT: A 478 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: D 23 GLN cc_start: 0.8918 (tp40) cc_final: 0.8521 (pt0) REVERT: D 24 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8209 (mm-40) REVERT: D 32 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7925 (ttm170) REVERT: D 42 TYR cc_start: 0.8249 (t80) cc_final: 0.8038 (t80) REVERT: D 46 LEU cc_start: 0.9020 (mp) cc_final: 0.8768 (tp) REVERT: D 115 ILE cc_start: 0.4439 (mt) cc_final: 0.4146 (mt) REVERT: D 127 LYS cc_start: 0.9410 (tppt) cc_final: 0.8994 (tppt) REVERT: D 167 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8276 (mmmt) REVERT: D 181 LEU cc_start: 0.7878 (tp) cc_final: 0.7585 (pp) REVERT: D 184 HIS cc_start: 0.6064 (m-70) cc_final: 0.5764 (m90) REVERT: D 185 ARG cc_start: 0.8465 (mmm160) cc_final: 0.7392 (mtm180) outliers start: 29 outliers final: 21 residues processed: 120 average time/residue: 0.0825 time to fit residues: 12.7834 Evaluate side-chains 119 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 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 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 235 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 358 ILE 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 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: 7.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 GLN A 516 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 95 GLN D 143 GLN D 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.169967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.129774 restraints weight = 14052.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134097 restraints weight = 7355.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137036 restraints weight = 4990.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138590 restraints weight = 3912.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139514 restraints weight = 3403.855| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6914 Z= 0.145 Angle : 0.570 7.517 9604 Z= 0.295 Chirality : 0.036 0.165 1096 Planarity : 0.004 0.040 1072 Dihedral : 12.286 99.138 1364 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.30 % Allowed : 22.55 % Favored : 73.15 % 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: 2.43 (0.33), residues: 707 helix: 2.81 (0.25), residues: 426 sheet: 0.04 (0.73), residues: 61 loop : -0.36 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.015 0.002 TYR D 42 PHE 0.007 0.001 PHE A 582 TRP 0.016 0.001 TRP A 450 HIS 0.015 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 6910) covalent geometry : angle 0.56952 / 0.30 ( 9601) hydrogen bonds : bond 0.04094 / 2.44 ( 402) hydrogen bonds : angle 4.16634 / 2.48 ( 1160) metal coordination : bond 0.00879 / 0.44 ( 4) metal coordination : angle 1.93701 / 0.65 ( 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 126 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.213 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: 0.8082 (mtt) cc_final: 0.7781 (mtm) REVERT: A 29 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: A 63 MET cc_start: 0.9050 (ptp) cc_final: 0.8371 (ptp) REVERT: A 119 LYS cc_start: 0.9007 (tptp) cc_final: 0.8796 (tppt) REVERT: A 127 LYS cc_start: 0.9365 (tmmt) cc_final: 0.9051 (tmmt) REVERT: A 138 LYS cc_start: 0.8530 (tptt) cc_final: 0.8144 (tptp) REVERT: A 185 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7214 (mtm180) REVERT: A 187 ASP cc_start: 0.8855 (p0) cc_final: 0.8586 (p0) REVERT: A 194 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7381 (p) REVERT: A 356 SER cc_start: 0.7529 (t) cc_final: 0.7261 (p) REVERT: A 475 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6902 (mm) REVERT: D 23 GLN cc_start: 0.8953 (tp40) cc_final: 0.8525 (pt0) REVERT: D 24 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8109 (mm-40) REVERT: D 42 TYR cc_start: 0.8070 (t80) cc_final: 0.7812 (t80) REVERT: D 137 GLN cc_start: 0.9028 (mt0) cc_final: 0.8797 (mm110) REVERT: D 138 LYS cc_start: 0.9211 (ptpt) cc_final: 0.8943 (ptpp) REVERT: D 185 ARG cc_start: 0.8483 (mmm160) cc_final: 0.7398 (mtm180) outliers start: 25 outliers final: 14 residues processed: 116 average time/residue: 0.0976 time to fit residues: 14.4491 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 185 ARG 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 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 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: 5.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 143 GLN D 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.167688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127498 restraints weight = 14154.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.131753 restraints weight = 7468.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134602 restraints weight = 5039.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136427 restraints weight = 3943.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137475 restraints weight = 3376.661| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6914 Z= 0.201 Angle : 0.635 7.620 9604 Z= 0.327 Chirality : 0.037 0.159 1096 Planarity : 0.004 0.040 1072 Dihedral : 12.413 98.862 1364 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.16 % Allowed : 23.06 % Favored : 71.77 % 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: 2.16 (0.33), residues: 707 helix: 2.57 (0.25), residues: 426 sheet: -0.22 (0.72), residues: 61 loop : -0.37 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 205 TYR 0.017 0.002 TYR A 217 PHE 0.006 0.001 PHE A 155 TRP 0.038 0.002 TRP D 50 HIS 0.014 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 6910) covalent geometry : angle 0.63313 / 0.33 ( 9601) hydrogen bonds : bond 0.04566 / 2.72 ( 402) hydrogen bonds : angle 4.34206 / 2.62 ( 1160) metal coordination : bond 0.01104 / 0.56 ( 4) metal coordination : angle 2.44308 / 0.81 ( 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: 30 poor density : 95 time to evaluate : 0.186 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: 0.8186 (mtt) cc_final: 0.7793 (mtm) REVERT: A 11 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 29 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7341 (t-90) REVERT: A 63 MET cc_start: 0.9103 (ptp) cc_final: 0.8770 (ptt) REVERT: A 127 LYS cc_start: 0.9400 (tmmt) cc_final: 0.9075 (tmmt) REVERT: A 475 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6986 (mm) REVERT: A 556 ASN cc_start: 0.8663 (m-40) cc_final: 0.8176 (m110) REVERT: D 23 GLN cc_start: 0.8934 (tp40) cc_final: 0.8543 (pt0) REVERT: D 32 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8047 (ttm-80) REVERT: D 42 TYR cc_start: 0.7976 (t80) cc_final: 0.7774 (t80) REVERT: D 50 TRP cc_start: 0.8435 (m100) cc_final: 0.7779 (m100) REVERT: D 115 ILE cc_start: 0.5064 (mt) cc_final: 0.4684 (mt) REVERT: D 137 GLN cc_start: 0.9054 (mt0) cc_final: 0.8825 (mm110) REVERT: D 185 ARG cc_start: 0.8562 (mmm160) cc_final: 0.7350 (mtm180) outliers start: 30 outliers final: 19 residues processed: 116 average time/residue: 0.0919 time to fit residues: 13.6934 Evaluate side-chains 112 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL 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 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 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 43 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 143 GLN D 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.175547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137421 restraints weight = 14481.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.141823 restraints weight = 7539.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.144819 restraints weight = 5032.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.146512 restraints weight = 3904.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.147510 restraints weight = 3344.535| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6914 Z= 0.129 Angle : 0.572 8.639 9604 Z= 0.299 Chirality : 0.036 0.165 1096 Planarity : 0.004 0.039 1072 Dihedral : 12.152 99.643 1364 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 4.30 % Allowed : 24.10 % Favored : 71.60 % 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: 2.26 (0.33), residues: 707 helix: 2.60 (0.25), residues: 426 sheet: -0.15 (0.72), residues: 61 loop : -0.23 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 129 TYR 0.014 0.002 TYR A 141 PHE 0.007 0.001 PHE A 582 TRP 0.026 0.002 TRP D 50 HIS 0.014 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6910) covalent geometry : angle 0.57092 / 0.30 ( 9601) hydrogen bonds : bond 0.03996 / 2.39 ( 402) hydrogen bonds : angle 4.14606 / 2.46 ( 1160) metal coordination : bond 0.00625 / 0.32 ( 4) metal coordination : angle 1.81427 / 0.60 ( 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 117 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.147 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: 0.8129 (mtt) cc_final: 0.7774 (mtm) REVERT: A 11 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8293 (t) REVERT: A 29 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: A 63 MET cc_start: 0.9021 (ptp) cc_final: 0.8340 (ptp) REVERT: A 127 LYS cc_start: 0.9409 (tmmt) cc_final: 0.9074 (tmmt) REVERT: A 138 LYS cc_start: 0.8566 (tptt) cc_final: 0.8204 (tptp) REVERT: A 187 ASP cc_start: 0.8683 (p0) cc_final: 0.8466 (p0) REVERT: A 194 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 556 ASN cc_start: 0.8643 (m-40) cc_final: 0.8380 (m-40) REVERT: D 23 GLN cc_start: 0.8958 (tp40) cc_final: 0.8537 (pt0) REVERT: D 42 TYR cc_start: 0.7925 (t80) cc_final: 0.7213 (t80) REVERT: D 50 TRP cc_start: 0.8438 (m100) cc_final: 0.8014 (m100) REVERT: D 53 TYR cc_start: 0.5370 (m-80) cc_final: 0.5152 (m-80) REVERT: D 154 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7762 (p) REVERT: D 185 ARG cc_start: 0.8530 (mmm160) cc_final: 0.7347 (mtm180) outliers start: 25 outliers final: 15 residues processed: 108 average time/residue: 0.0841 time to fit residues: 11.7009 Evaluate side-chains 106 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL 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 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 373 GLU 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 132 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 137 GLN D 143 GLN D 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.169589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.129803 restraints weight = 13858.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134161 restraints weight = 7300.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137033 restraints weight = 4919.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138671 restraints weight = 3833.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.139988 restraints weight = 3300.558| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4466 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= 0.146 Angle : 0.598 8.674 9604 Z= 0.313 Chirality : 0.037 0.161 1096 Planarity : 0.004 0.038 1072 Dihedral : 12.118 100.072 1364 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.48 % Allowed : 24.78 % 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: 2.17 (0.33), residues: 707 helix: 2.55 (0.25), residues: 426 sheet: -0.17 (0.72), residues: 61 loop : -0.32 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 125 TYR 0.013 0.001 TYR D 42 PHE 0.007 0.001 PHE A 582 TRP 0.019 0.002 TRP D 50 HIS 0.013 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6910) covalent geometry : angle 0.59732 / 0.31 ( 9601) hydrogen bonds : bond 0.03999 / 2.38 ( 402) hydrogen bonds : angle 4.16246 / 2.49 ( 1160) metal coordination : bond 0.00626 / 0.32 ( 4) metal coordination : angle 1.96272 / 0.65 ( 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: 26 poor density : 88 time to evaluate : 0.180 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: 0.8137 (mtt) cc_final: 0.7774 (mtm) REVERT: A 11 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8299 (t) REVERT: A 29 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7261 (t-90) REVERT: A 63 MET cc_start: 0.8999 (ptp) cc_final: 0.8380 (ptp) REVERT: A 127 LYS cc_start: 0.9408 (tmmt) cc_final: 0.9065 (tmmt) REVERT: A 138 LYS cc_start: 0.8571 (tptt) cc_final: 0.8221 (tptp) REVERT: A 194 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7340 (p) REVERT: A 356 SER cc_start: 0.7524 (t) cc_final: 0.7227 (p) REVERT: A 475 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6870 (mm) REVERT: A 556 ASN cc_start: 0.8547 (m110) cc_final: 0.8266 (m-40) REVERT: D 23 GLN cc_start: 0.8933 (tp40) cc_final: 0.8540 (pt0) REVERT: D 42 TYR cc_start: 0.7994 (t80) cc_final: 0.7404 (t80) REVERT: D 50 TRP cc_start: 0.8400 (m100) cc_final: 0.7797 (m100) REVERT: D 115 ILE cc_start: 0.4670 (mt) cc_final: 0.3993 (mt) REVERT: D 154 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7787 (p) REVERT: D 185 ARG cc_start: 0.8532 (mmm160) cc_final: 0.7345 (mtm180) outliers start: 26 outliers final: 18 residues processed: 105 average time/residue: 0.0830 time to fit residues: 11.4735 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL 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 60 GLU 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 208 MET 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 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 43 ASP Chi-restraints excluded: chain D residue 132 GLN 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: 1.9990 chunk 2 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.169718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129926 restraints weight = 14010.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134257 restraints weight = 7301.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137100 restraints weight = 4907.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.138749 restraints weight = 3822.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.139894 restraints weight = 3289.381| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4592 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= 0.150 Angle : 0.613 11.812 9604 Z= 0.313 Chirality : 0.037 0.185 1096 Planarity : 0.004 0.038 1072 Dihedral : 12.080 100.353 1364 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 2.10 (0.33), residues: 707 helix: 2.51 (0.25), residues: 426 sheet: -0.27 (0.72), residues: 61 loop : -0.34 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 125 TYR 0.013 0.002 TYR A 217 PHE 0.006 0.001 PHE A 582 TRP 0.051 0.002 TRP A 50 HIS 0.013 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 6910) covalent geometry : angle 0.61166 / 0.31 ( 9601) hydrogen bonds : bond 0.03958 / 2.35 ( 402) hydrogen bonds : angle 4.17782 / 2.50 ( 1160) metal coordination : bond 0.00558 / 0.29 ( 4) metal coordination : angle 1.96391 / 0.65 ( 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: 27 poor density : 85 time to evaluate : 0.222 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: A 9 MET cc_start: 0.8139 (mtt) cc_final: 0.7774 (mtm) REVERT: A 11 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8303 (t) REVERT: A 29 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: A 63 MET cc_start: 0.8999 (ptp) cc_final: 0.8424 (ptp) REVERT: A 127 LYS cc_start: 0.9425 (tmmt) cc_final: 0.9093 (tmmt) REVERT: A 138 LYS cc_start: 0.8558 (tptt) cc_final: 0.8220 (tptp) REVERT: A 194 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7351 (p) REVERT: A 475 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6898 (mm) REVERT: A 556 ASN cc_start: 0.8594 (m110) cc_final: 0.8295 (m-40) REVERT: D 42 TYR cc_start: 0.8066 (t80) cc_final: 0.7484 (t80) REVERT: D 50 TRP cc_start: 0.8392 (m100) cc_final: 0.7924 (m100) REVERT: D 185 ARG cc_start: 0.8538 (mmm160) cc_final: 0.7345 (mtm180) outliers start: 27 outliers final: 21 residues processed: 103 average time/residue: 0.0657 time to fit residues: 9.2491 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL 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 60 GLU 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 208 MET 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 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 43 ASP Chi-restraints excluded: chain D residue 132 GLN 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: 0.5980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 72 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 ** 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 = 0.4432 r_free = 0.4432 target = 0.171612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.132358 restraints weight = 14019.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.136725 restraints weight = 7284.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.139628 restraints weight = 4863.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141236 restraints weight = 3779.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.142528 restraints weight = 3256.644| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6914 Z= 0.117 Angle : 0.578 9.448 9604 Z= 0.299 Chirality : 0.037 0.189 1096 Planarity : 0.004 0.038 1072 Dihedral : 11.877 100.824 1364 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.61 % Allowed : 26.16 % Favored : 70.22 % 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: 2.16 (0.33), residues: 707 helix: 2.55 (0.25), residues: 432 sheet: -0.28 (0.71), residues: 62 loop : -0.41 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 125 TYR 0.015 0.001 TYR A 141 PHE 0.013 0.001 PHE A 582 TRP 0.020 0.001 TRP D 50 HIS 0.012 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6910) covalent geometry : angle 0.57778 / 0.30 ( 9601) hydrogen bonds : bond 0.03655 / 2.17 ( 402) hydrogen bonds : angle 4.06785 / 2.41 ( 1160) metal coordination : bond 0.00402 / 0.22 ( 4) metal coordination : angle 1.55590 / 0.52 ( 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 115 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.335 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: 0.7832 (mtt) cc_final: 0.7478 (mtm) REVERT: A 11 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (t) REVERT: A 29 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: A 63 MET cc_start: 0.8961 (ptp) cc_final: 0.8413 (ptp) REVERT: A 127 LYS cc_start: 0.9413 (tmmt) cc_final: 0.9076 (tmmt) REVERT: A 194 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7371 (p) REVERT: A 556 ASN cc_start: 0.8452 (m110) cc_final: 0.7878 (m110) REVERT: A 568 ARG cc_start: 0.7475 (tpp80) cc_final: 0.6696 (tpp80) REVERT: A 575 MET cc_start: 0.8194 (tpp) cc_final: 0.7722 (tpp) REVERT: D 42 TYR cc_start: 0.8237 (t80) cc_final: 0.7561 (t80) REVERT: D 44 ASP cc_start: 0.9167 (m-30) cc_final: 0.8709 (p0) REVERT: D 50 TRP cc_start: 0.8232 (m100) cc_final: 0.7617 (m100) REVERT: D 185 ARG cc_start: 0.8465 (mmm160) cc_final: 0.7315 (mtm180) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 0.0721 time to fit residues: 10.2076 Evaluate side-chains 100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 60 GLU 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 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 132 GLN 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 36 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.0370 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 overall best weight: 3.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 HIS D 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.169944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129963 restraints weight = 13967.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134260 restraints weight = 7359.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137169 restraints weight = 4950.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139014 restraints weight = 3864.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140033 restraints weight = 3296.282| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6914 Z= 0.153 Angle : 0.612 9.437 9604 Z= 0.316 Chirality : 0.037 0.193 1096 Planarity : 0.004 0.038 1072 Dihedral : 11.971 100.613 1364 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 26.68 % Favored : 70.05 % 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: 2.10 (0.33), residues: 707 helix: 2.48 (0.25), residues: 431 sheet: -0.20 (0.72), residues: 61 loop : -0.39 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.013 0.001 TYR D 141 PHE 0.020 0.002 PHE A 582 TRP 0.044 0.002 TRP A 50 HIS 0.013 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6910) covalent geometry : angle 0.61140 / 0.32 ( 9601) hydrogen bonds : bond 0.03927 / 2.34 ( 402) hydrogen bonds : angle 4.19341 / 2.52 ( 1160) metal coordination : bond 0.00635 / 0.33 ( 4) metal coordination : angle 1.96086 / 0.65 ( 3) =============================================================================== Job complete usr+sys time: 1303.66 seconds wall clock time: 23 minutes 7.83 seconds (1387.83 seconds total)