Starting phenix.real_space_refine on Thu Jul 2 02:13:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.map" model { file = "/net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qsc_53335/07_2026/9qsc_53335.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 16 5.16 5 C 3529 2.51 5 N 949 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 5601 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5194 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 9, 'TRANS': 616} Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 1.23, per 1000 atoms: 0.22 Number of scatterers: 5601 At special positions: 0 Unit cell: (71.02, 89.04, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 19 15.00 O 1088 8.00 N 949 7.00 C 3529 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: 0.47 Conformation dependent library (CDL) restraints added in 190.1 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 55.9% alpha, 12.6% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.807A pdb=" N ASN A 70 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.506A pdb=" N LYS A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.817A pdb=" N ASP A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 206 through 234 removed outlier: 4.639A pdb=" N LEU A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 260 through 287 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.918A pdb=" N ASN A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 327 " --> pdb=" O ASN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 removed outlier: 3.523A pdb=" N ILE A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.543A pdb=" N ILE A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.522A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.749A pdb=" N PHE A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.137A pdb=" N LYS A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.539A pdb=" N HIS A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.600A pdb=" N TYR A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 566 Proline residue: A 546 - end of helix removed outlier: 3.625A pdb=" N ASP A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 609 removed outlier: 3.797A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 29 removed outlier: 3.619A pdb=" N ASP A 24 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 60 removed outlier: 6.329A pdb=" N LYS A 135 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.726A pdb=" N LYS A 258 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.888A pdb=" N THR A 367 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 577 removed outlier: 6.856A pdb=" N ILE A 582 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS A 576 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 523 through 525 269 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1652 1.33 - 1.45: 840 1.45 - 1.57: 3183 1.57 - 1.69: 37 1.69 - 1.81: 23 Bond restraints: 5735 Sorted by residual: bond pdb=" C1' DT C 11 " pdb=" N1 DT C 11 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.78e+01 bond pdb=" C3' DC B 15 " pdb=" C2' DC B 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C3' DC C 12 " pdb=" C2' DC C 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 bond pdb=" C3' DT B 22 " pdb=" C2' DT B 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.71e+00 ... (remaining 5730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 7580 1.41 - 2.83: 201 2.83 - 4.24: 14 4.24 - 5.66: 7 5.66 - 7.07: 5 Bond angle restraints: 7807 Sorted by residual: angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT B 22 " pdb=" C4 DT B 22 " pdb=" O4 DT B 22 " ideal model delta sigma weight residual 119.90 122.23 -2.33 6.00e-01 2.78e+00 1.50e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.16 -2.26 6.00e-01 2.78e+00 1.42e+01 angle pdb=" O4 DT C 18 " pdb=" C4 DT C 18 " pdb=" C5 DT C 18 " ideal model delta sigma weight residual 124.90 122.29 2.61 7.00e-01 2.04e+00 1.39e+01 ... (remaining 7802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 3132 16.91 - 33.82: 229 33.82 - 50.73: 71 50.73 - 67.63: 31 67.63 - 84.54: 2 Dihedral angle restraints: 3465 sinusoidal: 1585 harmonic: 1880 Sorted by residual: dihedral pdb=" CA LYS A 382 " pdb=" C LYS A 382 " pdb=" N PRO A 383 " pdb=" CA PRO A 383 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LYS A 417 " pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " pdb=" CD LYS A 417 " ideal model delta sinusoidal sigma weight residual -180.00 -121.28 -58.72 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A 224 " pdb=" CG LYS A 224 " pdb=" CD LYS A 224 " pdb=" CE LYS A 224 " ideal model delta sinusoidal sigma weight residual -180.00 -124.97 -55.03 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 3462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 866 0.130 - 0.260: 7 0.260 - 0.390: 0 0.390 - 0.519: 0 0.519 - 0.649: 3 Chirality restraints: 876 Sorted by residual: chirality pdb=" P DA B 24 " pdb=" OP1 DA B 24 " pdb=" OP2 DA B 24 " pdb=" O5' DA B 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC C 17 " pdb=" OP1 DC C 17 " pdb=" OP2 DC C 17 " pdb=" O5' DC C 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" P DA C 16 " pdb=" OP1 DA C 16 " pdb=" OP2 DA C 16 " pdb=" O5' DA C 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.79e+00 ... (remaining 873 not shown) Planarity restraints: 929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 247 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 248 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 382 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 383 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 383 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 383 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 353 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 354 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.016 5.00e-02 4.00e+02 ... (remaining 926 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 83 2.67 - 3.22: 5391 3.22 - 3.78: 8329 3.78 - 4.34: 11551 4.34 - 4.90: 18668 Nonbonded interactions: 44022 Sorted by model distance: nonbonded pdb=" OE1 GLN A 296 " pdb=" OG1 THR A 319 " model vdw 2.106 3.040 nonbonded pdb=" O LYS A 305 " pdb=" ND2 ASN A 307 " model vdw 2.239 3.120 nonbonded pdb=" O ASP A 16 " pdb=" ND2 ASN A 18 " model vdw 2.254 3.120 nonbonded pdb=" NZ LYS A 283 " pdb=" O ILE A 291 " model vdw 2.267 3.120 nonbonded pdb=" OD1 ASN A 205 " pdb=" NE2 GLN A 208 " model vdw 2.294 3.120 ... (remaining 44017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.004 0.074 5735 Z= 0.276 Angle : 0.565 7.069 7807 Z= 0.372 Chirality : 0.055 0.649 876 Planarity : 0.003 0.044 929 Dihedral : 14.159 84.542 2241 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 0.34 % Allowed : 2.89 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.34), residues: 624 helix: 1.18 (0.30), residues: 301 sheet: -0.52 (0.64), residues: 64 loop : -0.06 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 459 TYR 0.011 0.001 TYR A 499 PHE 0.012 0.002 PHE A 406 TRP 0.004 0.001 TRP A 199 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.28 ( 5735) covalent geometry : angle 0.56467 / 0.37 ( 7807) hydrogen bonds : bond 0.16856 / 10.86 ( 290) hydrogen bonds : angle 7.15022 / 4.83 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8681 (mttt) cc_final: 0.8289 (mtmm) REVERT: A 21 LYS cc_start: 0.8610 (tttp) cc_final: 0.8394 (tttt) REVERT: A 29 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8322 (mmmt) REVERT: A 30 ASN cc_start: 0.8258 (t0) cc_final: 0.8025 (t0) REVERT: A 35 ILE cc_start: 0.8855 (mt) cc_final: 0.7871 (mt) REVERT: A 47 LYS cc_start: 0.8487 (tttt) cc_final: 0.8085 (tttt) REVERT: A 55 SER cc_start: 0.8352 (p) cc_final: 0.8137 (m) REVERT: A 64 ASN cc_start: 0.8149 (t0) cc_final: 0.7692 (t0) REVERT: A 68 ASN cc_start: 0.8576 (m-40) cc_final: 0.8374 (m-40) REVERT: A 89 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 117 LYS cc_start: 0.8099 (mttm) cc_final: 0.7805 (mttm) REVERT: A 143 ASP cc_start: 0.7888 (m-30) cc_final: 0.7612 (m-30) REVERT: A 177 LYS cc_start: 0.8135 (mttp) cc_final: 0.7874 (mttt) REVERT: A 201 ASN cc_start: 0.8065 (t0) cc_final: 0.7847 (t0) REVERT: A 203 LEU cc_start: 0.8159 (mt) cc_final: 0.7857 (mt) REVERT: A 205 ASN cc_start: 0.7832 (p0) cc_final: 0.7625 (p0) REVERT: A 206 ASN cc_start: 0.8063 (t0) cc_final: 0.7790 (t0) REVERT: A 260 ASP cc_start: 0.7963 (t0) cc_final: 0.7519 (t0) REVERT: A 280 ASP cc_start: 0.8053 (t0) cc_final: 0.7725 (t0) REVERT: A 289 GLU cc_start: 0.7907 (pp20) cc_final: 0.7672 (pp20) REVERT: A 319 THR cc_start: 0.7496 (p) cc_final: 0.6768 (p) REVERT: A 412 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8323 (mtmm) REVERT: A 425 ASP cc_start: 0.7867 (t0) cc_final: 0.7578 (t0) REVERT: A 428 MET cc_start: 0.8390 (mtt) cc_final: 0.8131 (mtt) REVERT: A 430 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8166 (ttmm) REVERT: A 450 ASN cc_start: 0.7455 (t0) cc_final: 0.7203 (t0) REVERT: A 455 ASN cc_start: 0.7955 (p0) cc_final: 0.7440 (p0) REVERT: A 463 LYS cc_start: 0.8001 (tptm) cc_final: 0.7436 (tppp) REVERT: A 494 GLN cc_start: 0.8261 (mt0) cc_final: 0.7588 (mt0) REVERT: A 499 TYR cc_start: 0.8472 (t80) cc_final: 0.8222 (t80) REVERT: A 517 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8272 (ttmm) REVERT: A 519 LYS cc_start: 0.8661 (tppp) cc_final: 0.8411 (tppt) REVERT: A 524 TYR cc_start: 0.8063 (m-80) cc_final: 0.7713 (m-80) REVERT: A 580 GLU cc_start: 0.8074 (tt0) cc_final: 0.7823 (tt0) outliers start: 2 outliers final: 2 residues processed: 212 average time/residue: 0.0920 time to fit residues: 23.9270 Evaluate side-chains 195 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 374 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 170 ASN A 307 ASN A 386 GLN A 480 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119528 restraints weight = 7965.123| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.14 r_work: 0.3397 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5735 Z= 0.191 Angle : 0.583 6.325 7807 Z= 0.338 Chirality : 0.047 0.155 876 Planarity : 0.004 0.047 929 Dihedral : 15.886 59.911 887 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.76 % Favored : 98.08 % Rotamer: Outliers : 2.38 % Allowed : 10.53 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.34), residues: 624 helix: 1.32 (0.30), residues: 298 sheet: -0.55 (0.56), residues: 74 loop : 0.45 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 340 TYR 0.023 0.002 TYR A 475 PHE 0.023 0.002 PHE A 502 TRP 0.007 0.002 TRP A 624 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 5735) covalent geometry : angle 0.58326 / 0.34 ( 7807) hydrogen bonds : bond 0.05671 / 3.65 ( 290) hydrogen bonds : angle 5.18711 / 3.58 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.158 Fit side-chains REVERT: A 17 ASP cc_start: 0.7977 (t0) cc_final: 0.7739 (t0) REVERT: A 29 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8096 (mmmt) REVERT: A 30 ASN cc_start: 0.8217 (t0) cc_final: 0.7887 (p0) REVERT: A 35 ILE cc_start: 0.8632 (mt) cc_final: 0.8322 (mt) REVERT: A 47 LYS cc_start: 0.8542 (tttt) cc_final: 0.8225 (tttt) REVERT: A 64 ASN cc_start: 0.8185 (t0) cc_final: 0.7734 (t0) REVERT: A 89 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 97 LEU cc_start: 0.8293 (mt) cc_final: 0.8019 (mt) REVERT: A 117 LYS cc_start: 0.8169 (mttm) cc_final: 0.7827 (mttm) REVERT: A 136 ILE cc_start: 0.8130 (mm) cc_final: 0.7905 (mt) REVERT: A 143 ASP cc_start: 0.7722 (m-30) cc_final: 0.7501 (m-30) REVERT: A 201 ASN cc_start: 0.8008 (t0) cc_final: 0.7776 (t0) REVERT: A 203 LEU cc_start: 0.8268 (mt) cc_final: 0.8060 (mp) REVERT: A 205 ASN cc_start: 0.8028 (p0) cc_final: 0.7770 (p0) REVERT: A 280 ASP cc_start: 0.8129 (t0) cc_final: 0.7757 (t0) REVERT: A 292 ASN cc_start: 0.7886 (t0) cc_final: 0.7535 (t0) REVERT: A 319 THR cc_start: 0.7623 (p) cc_final: 0.7350 (p) REVERT: A 339 TYR cc_start: 0.8483 (t80) cc_final: 0.8215 (t80) REVERT: A 380 SER cc_start: 0.8285 (p) cc_final: 0.8009 (p) REVERT: A 410 ASP cc_start: 0.7395 (p0) cc_final: 0.7168 (p0) REVERT: A 412 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8360 (mtmm) REVERT: A 430 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8215 (ttmm) REVERT: A 447 THR cc_start: 0.8691 (p) cc_final: 0.8284 (t) REVERT: A 463 LYS cc_start: 0.7975 (tptm) cc_final: 0.7458 (tppp) REVERT: A 477 ASN cc_start: 0.7801 (t0) cc_final: 0.7572 (t0) REVERT: A 479 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7867 (tptt) REVERT: A 490 MET cc_start: 0.7803 (mmm) cc_final: 0.7538 (mmm) REVERT: A 517 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8113 (ttmm) REVERT: A 575 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 580 GLU cc_start: 0.8220 (tt0) cc_final: 0.7991 (tt0) outliers start: 14 outliers final: 7 residues processed: 206 average time/residue: 0.0862 time to fit residues: 22.0724 Evaluate side-chains 200 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 139 ASN A 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119892 restraints weight = 7916.207| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.14 r_work: 0.3397 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5735 Z= 0.167 Angle : 0.535 6.078 7807 Z= 0.313 Chirality : 0.045 0.139 876 Planarity : 0.004 0.052 929 Dihedral : 15.889 59.927 885 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.60 % Favored : 98.24 % Rotamer: Outliers : 2.38 % Allowed : 13.24 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.34), residues: 624 helix: 1.39 (0.30), residues: 298 sheet: -0.38 (0.59), residues: 72 loop : 0.25 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.026 0.001 TYR A 475 PHE 0.019 0.002 PHE A 502 TRP 0.006 0.001 TRP A 512 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 5735) covalent geometry : angle 0.53519 / 0.31 ( 7807) hydrogen bonds : bond 0.04943 / 3.21 ( 290) hydrogen bonds : angle 4.95354 / 3.43 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.175 Fit side-chains REVERT: A 9 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8199 (tppt) REVERT: A 30 ASN cc_start: 0.8163 (t0) cc_final: 0.7764 (p0) REVERT: A 36 THR cc_start: 0.8678 (t) cc_final: 0.8282 (p) REVERT: A 64 ASN cc_start: 0.8103 (t0) cc_final: 0.7639 (t0) REVERT: A 89 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 96 ARG cc_start: 0.7928 (tpt90) cc_final: 0.7724 (tpt170) REVERT: A 117 LYS cc_start: 0.8104 (mttm) cc_final: 0.7732 (mttm) REVERT: A 136 ILE cc_start: 0.8137 (mm) cc_final: 0.7931 (mt) REVERT: A 143 ASP cc_start: 0.7713 (m-30) cc_final: 0.7497 (m-30) REVERT: A 201 ASN cc_start: 0.8033 (t0) cc_final: 0.7708 (t0) REVERT: A 203 LEU cc_start: 0.8272 (mt) cc_final: 0.8054 (mp) REVERT: A 233 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 280 ASP cc_start: 0.8136 (t0) cc_final: 0.7770 (t0) REVERT: A 285 LYS cc_start: 0.8056 (mttm) cc_final: 0.7481 (mttm) REVERT: A 286 LEU cc_start: 0.9007 (mt) cc_final: 0.8756 (mp) REVERT: A 292 ASN cc_start: 0.7906 (t0) cc_final: 0.7349 (t0) REVERT: A 319 THR cc_start: 0.7672 (p) cc_final: 0.7216 (p) REVERT: A 332 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 380 SER cc_start: 0.8257 (p) cc_final: 0.7972 (p) REVERT: A 410 ASP cc_start: 0.7405 (p0) cc_final: 0.7171 (p0) REVERT: A 412 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8339 (mtmm) REVERT: A 425 ASP cc_start: 0.7699 (t0) cc_final: 0.7453 (t0) REVERT: A 430 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8179 (ttmm) REVERT: A 463 LYS cc_start: 0.7985 (tptm) cc_final: 0.7476 (tppp) REVERT: A 479 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7856 (tptt) REVERT: A 490 MET cc_start: 0.7803 (mmm) cc_final: 0.7468 (mmm) REVERT: A 517 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8174 (ttmm) REVERT: A 580 GLU cc_start: 0.8185 (tt0) cc_final: 0.7872 (tt0) outliers start: 14 outliers final: 8 residues processed: 201 average time/residue: 0.0816 time to fit residues: 20.2996 Evaluate side-chains 197 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 170 ASN A 318 ASN A 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119447 restraints weight = 7882.690| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.10 r_work: 0.3395 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5735 Z= 0.183 Angle : 0.533 5.916 7807 Z= 0.310 Chirality : 0.045 0.141 876 Planarity : 0.004 0.054 929 Dihedral : 15.947 59.973 885 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 2.72 % Allowed : 15.45 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.34), residues: 624 helix: 1.43 (0.30), residues: 301 sheet: -0.28 (0.60), residues: 72 loop : 0.18 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.028 0.001 TYR A 65 PHE 0.017 0.002 PHE A 502 TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 5735) covalent geometry : angle 0.53296 / 0.31 ( 7807) hydrogen bonds : bond 0.04695 / 3.03 ( 290) hydrogen bonds : angle 4.85744 / 3.37 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.175 Fit side-chains REVERT: A 9 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8352 (tppt) REVERT: A 30 ASN cc_start: 0.8225 (t0) cc_final: 0.7726 (p0) REVERT: A 36 THR cc_start: 0.8660 (t) cc_final: 0.8266 (p) REVERT: A 64 ASN cc_start: 0.8422 (t0) cc_final: 0.8090 (t0) REVERT: A 74 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8320 (tptp) REVERT: A 89 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 117 LYS cc_start: 0.8192 (mttm) cc_final: 0.7837 (mttm) REVERT: A 136 ILE cc_start: 0.8270 (mm) cc_final: 0.8063 (mt) REVERT: A 143 ASP cc_start: 0.7971 (m-30) cc_final: 0.7745 (m-30) REVERT: A 201 ASN cc_start: 0.8200 (t0) cc_final: 0.7964 (t0) REVERT: A 203 LEU cc_start: 0.8332 (mt) cc_final: 0.8112 (mp) REVERT: A 233 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7709 (mm-30) REVERT: A 280 ASP cc_start: 0.8333 (t0) cc_final: 0.7985 (t0) REVERT: A 285 LYS cc_start: 0.8182 (mttm) cc_final: 0.7717 (mttm) REVERT: A 292 ASN cc_start: 0.8081 (t0) cc_final: 0.7880 (t0) REVERT: A 293 VAL cc_start: 0.8489 (t) cc_final: 0.8284 (p) REVERT: A 319 THR cc_start: 0.7739 (p) cc_final: 0.7377 (p) REVERT: A 380 SER cc_start: 0.8244 (p) cc_final: 0.7928 (p) REVERT: A 410 ASP cc_start: 0.7668 (p0) cc_final: 0.7408 (p0) REVERT: A 412 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8440 (mtmm) REVERT: A 425 ASP cc_start: 0.7858 (t0) cc_final: 0.7597 (t0) REVERT: A 430 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8316 (ttmm) REVERT: A 447 THR cc_start: 0.8849 (p) cc_final: 0.8466 (t) REVERT: A 463 LYS cc_start: 0.8151 (tptm) cc_final: 0.7796 (tptm) REVERT: A 474 ASN cc_start: 0.8405 (t0) cc_final: 0.8052 (t0) REVERT: A 517 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8207 (ttmm) REVERT: A 580 GLU cc_start: 0.8278 (tt0) cc_final: 0.7945 (tt0) REVERT: A 584 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7630 (mt-10) outliers start: 16 outliers final: 11 residues processed: 198 average time/residue: 0.0852 time to fit residues: 20.8072 Evaluate side-chains 197 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117070 restraints weight = 7965.255| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.08 r_work: 0.3348 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 5735 Z= 0.305 Angle : 0.609 7.982 7807 Z= 0.343 Chirality : 0.048 0.155 876 Planarity : 0.004 0.064 929 Dihedral : 16.018 59.284 885 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 3.06 % Allowed : 16.13 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.34), residues: 624 helix: 1.08 (0.30), residues: 309 sheet: -0.24 (0.60), residues: 74 loop : 0.03 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.028 0.002 TYR A 475 PHE 0.019 0.003 PHE A 502 TRP 0.006 0.002 TRP A 624 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.31 ( 5735) covalent geometry : angle 0.60891 / 0.34 ( 7807) hydrogen bonds : bond 0.05214 / 3.35 ( 290) hydrogen bonds : angle 4.90858 / 3.40 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.201 Fit side-chains REVERT: A 9 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8351 (tppt) REVERT: A 30 ASN cc_start: 0.8239 (t0) cc_final: 0.7714 (p0) REVERT: A 36 THR cc_start: 0.8654 (t) cc_final: 0.8232 (p) REVERT: A 89 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 117 LYS cc_start: 0.8256 (mttm) cc_final: 0.7922 (mttm) REVERT: A 143 ASP cc_start: 0.7998 (m-30) cc_final: 0.7772 (m-30) REVERT: A 201 ASN cc_start: 0.8225 (t0) cc_final: 0.7970 (t0) REVERT: A 203 LEU cc_start: 0.8355 (mt) cc_final: 0.8103 (mp) REVERT: A 233 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 260 ASP cc_start: 0.8048 (t0) cc_final: 0.7458 (t0) REVERT: A 280 ASP cc_start: 0.8395 (t0) cc_final: 0.8037 (t0) REVERT: A 292 ASN cc_start: 0.8279 (t0) cc_final: 0.8061 (t0) REVERT: A 293 VAL cc_start: 0.8614 (t) cc_final: 0.8405 (p) REVERT: A 319 THR cc_start: 0.7794 (p) cc_final: 0.7244 (p) REVERT: A 340 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8434 (tpp80) REVERT: A 410 ASP cc_start: 0.7646 (p0) cc_final: 0.7388 (p0) REVERT: A 412 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8434 (mtmm) REVERT: A 425 ASP cc_start: 0.7853 (t0) cc_final: 0.7581 (t0) REVERT: A 430 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8369 (ttmm) REVERT: A 447 THR cc_start: 0.8821 (p) cc_final: 0.8454 (t) REVERT: A 463 LYS cc_start: 0.8263 (tptm) cc_final: 0.7752 (tppp) REVERT: A 474 ASN cc_start: 0.8418 (t0) cc_final: 0.7987 (t0) REVERT: A 479 LYS cc_start: 0.8207 (tptt) cc_final: 0.7984 (tptt) REVERT: A 490 MET cc_start: 0.8112 (mmm) cc_final: 0.7650 (mmm) REVERT: A 580 GLU cc_start: 0.8299 (tt0) cc_final: 0.8056 (tt0) REVERT: A 584 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7607 (mt-10) outliers start: 18 outliers final: 13 residues processed: 197 average time/residue: 0.0939 time to fit residues: 22.8561 Evaluate side-chains 201 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 170 ASN A 180 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 297 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119301 restraints weight = 7886.083| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.12 r_work: 0.3393 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5735 Z= 0.142 Angle : 0.549 6.709 7807 Z= 0.310 Chirality : 0.044 0.149 876 Planarity : 0.004 0.056 929 Dihedral : 16.036 59.926 885 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 2.72 % Allowed : 18.17 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.34), residues: 624 helix: 1.40 (0.30), residues: 301 sheet: -0.20 (0.61), residues: 74 loop : 0.08 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.028 0.001 TYR A 475 PHE 0.028 0.002 PHE A 537 TRP 0.006 0.001 TRP A 512 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5735) covalent geometry : angle 0.54873 / 0.31 ( 7807) hydrogen bonds : bond 0.04531 / 2.91 ( 290) hydrogen bonds : angle 4.74582 / 3.30 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.231 Fit side-chains REVERT: A 9 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8375 (tppt) REVERT: A 30 ASN cc_start: 0.8223 (t0) cc_final: 0.8013 (t0) REVERT: A 74 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8312 (tptp) REVERT: A 89 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 96 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7853 (tpt170) REVERT: A 112 MET cc_start: 0.8169 (mmt) cc_final: 0.7773 (mmt) REVERT: A 117 LYS cc_start: 0.8277 (mttm) cc_final: 0.7934 (mttm) REVERT: A 143 ASP cc_start: 0.7976 (m-30) cc_final: 0.7746 (m-30) REVERT: A 201 ASN cc_start: 0.8240 (t0) cc_final: 0.7873 (t0) REVERT: A 203 LEU cc_start: 0.8355 (mt) cc_final: 0.8097 (mp) REVERT: A 233 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 260 ASP cc_start: 0.8020 (t0) cc_final: 0.7470 (t0) REVERT: A 280 ASP cc_start: 0.8313 (t0) cc_final: 0.7936 (t0) REVERT: A 285 LYS cc_start: 0.8094 (mttm) cc_final: 0.7757 (mttm) REVERT: A 292 ASN cc_start: 0.8161 (t0) cc_final: 0.7739 (t0) REVERT: A 293 VAL cc_start: 0.8555 (t) cc_final: 0.8282 (p) REVERT: A 319 THR cc_start: 0.7816 (p) cc_final: 0.7477 (p) REVERT: A 332 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 380 SER cc_start: 0.8243 (p) cc_final: 0.7929 (p) REVERT: A 410 ASP cc_start: 0.7659 (p0) cc_final: 0.7411 (p0) REVERT: A 412 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8422 (mtmm) REVERT: A 428 MET cc_start: 0.8456 (mtt) cc_final: 0.8160 (mtt) REVERT: A 430 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8346 (ttmm) REVERT: A 447 THR cc_start: 0.8858 (p) cc_final: 0.8482 (t) REVERT: A 463 LYS cc_start: 0.8161 (tptm) cc_final: 0.7682 (tppp) REVERT: A 474 ASN cc_start: 0.8421 (t0) cc_final: 0.7961 (t0) REVERT: A 479 LYS cc_start: 0.8169 (tptt) cc_final: 0.7935 (tptt) REVERT: A 490 MET cc_start: 0.8132 (mmm) cc_final: 0.7689 (mmm) REVERT: A 580 GLU cc_start: 0.8318 (tt0) cc_final: 0.8073 (tt0) REVERT: A 584 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7585 (mt-10) outliers start: 16 outliers final: 12 residues processed: 195 average time/residue: 0.0877 time to fit residues: 21.3549 Evaluate side-chains 202 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0010 chunk 47 optimal weight: 0.9990 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.142394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119221 restraints weight = 8026.918| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.13 r_work: 0.3391 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5735 Z= 0.154 Angle : 0.550 6.568 7807 Z= 0.311 Chirality : 0.045 0.155 876 Planarity : 0.004 0.064 929 Dihedral : 16.037 58.962 885 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 3.23 % Allowed : 18.00 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.34), residues: 624 helix: 1.48 (0.30), residues: 301 sheet: -0.20 (0.58), residues: 84 loop : 0.10 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.008 0.001 TYR A 339 PHE 0.015 0.002 PHE A 58 TRP 0.006 0.001 TRP A 512 HIS 0.002 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5735) covalent geometry : angle 0.54973 / 0.31 ( 7807) hydrogen bonds : bond 0.04338 / 2.76 ( 290) hydrogen bonds : angle 4.64731 / 3.23 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.200 Fit side-chains REVERT: A 9 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8229 (tppt) REVERT: A 74 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8183 (tptp) REVERT: A 89 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 96 ARG cc_start: 0.7934 (tpt90) cc_final: 0.7590 (tpt-90) REVERT: A 103 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 117 LYS cc_start: 0.8203 (mttm) cc_final: 0.7764 (mttm) REVERT: A 143 ASP cc_start: 0.7761 (m-30) cc_final: 0.7548 (m-30) REVERT: A 201 ASN cc_start: 0.8105 (t0) cc_final: 0.7475 (t0) REVERT: A 203 LEU cc_start: 0.8320 (mt) cc_final: 0.8042 (mp) REVERT: A 233 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 260 ASP cc_start: 0.7911 (t0) cc_final: 0.7352 (t0) REVERT: A 287 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8253 (mtpp) REVERT: A 292 ASN cc_start: 0.8048 (t0) cc_final: 0.7596 (t0) REVERT: A 319 THR cc_start: 0.7876 (p) cc_final: 0.7553 (p) REVERT: A 323 ASN cc_start: 0.7515 (t0) cc_final: 0.6995 (t0) REVERT: A 380 SER cc_start: 0.8163 (p) cc_final: 0.7816 (p) REVERT: A 410 ASP cc_start: 0.7438 (p0) cc_final: 0.7197 (p0) REVERT: A 412 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8428 (mtmm) REVERT: A 428 MET cc_start: 0.8244 (mtt) cc_final: 0.7876 (mtt) REVERT: A 430 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8217 (ttmm) REVERT: A 447 THR cc_start: 0.8746 (p) cc_final: 0.8356 (t) REVERT: A 463 LYS cc_start: 0.8065 (tptm) cc_final: 0.7550 (tppp) REVERT: A 474 ASN cc_start: 0.8218 (t0) cc_final: 0.7736 (t0) REVERT: A 479 LYS cc_start: 0.8014 (tptt) cc_final: 0.7769 (tptt) REVERT: A 490 MET cc_start: 0.7658 (mmm) cc_final: 0.7219 (mmm) REVERT: A 580 GLU cc_start: 0.8221 (tt0) cc_final: 0.7986 (tt0) REVERT: A 584 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7234 (mt-10) outliers start: 19 outliers final: 13 residues processed: 199 average time/residue: 0.0829 time to fit residues: 20.4384 Evaluate side-chains 203 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 139 ASN A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119201 restraints weight = 7870.537| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.10 r_work: 0.3390 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5735 Z= 0.165 Angle : 0.551 6.000 7807 Z= 0.310 Chirality : 0.044 0.150 876 Planarity : 0.003 0.057 929 Dihedral : 15.959 59.861 885 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.57 % Allowed : 18.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.34), residues: 624 helix: 1.48 (0.30), residues: 301 sheet: -0.16 (0.61), residues: 74 loop : -0.02 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 340 TYR 0.009 0.001 TYR A 223 PHE 0.027 0.002 PHE A 537 TRP 0.005 0.001 TRP A 199 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5735) covalent geometry : angle 0.55066 / 0.31 ( 7807) hydrogen bonds : bond 0.04337 / 2.77 ( 290) hydrogen bonds : angle 4.60827 / 3.21 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.204 Fit side-chains REVERT: A 9 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8372 (tppt) REVERT: A 74 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8356 (tptp) REVERT: A 89 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 103 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 117 LYS cc_start: 0.8299 (mttm) cc_final: 0.7862 (mttm) REVERT: A 143 ASP cc_start: 0.7990 (m-30) cc_final: 0.7750 (m-30) REVERT: A 201 ASN cc_start: 0.8263 (t0) cc_final: 0.7979 (t0) REVERT: A 203 LEU cc_start: 0.8366 (mt) cc_final: 0.8103 (mp) REVERT: A 233 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 260 ASP cc_start: 0.8036 (t0) cc_final: 0.7544 (t0) REVERT: A 292 ASN cc_start: 0.8219 (t0) cc_final: 0.7789 (t0) REVERT: A 319 THR cc_start: 0.7877 (p) cc_final: 0.7525 (p) REVERT: A 323 ASN cc_start: 0.7640 (t0) cc_final: 0.7152 (t0) REVERT: A 332 GLU cc_start: 0.8225 (tp30) cc_final: 0.7859 (mm-30) REVERT: A 377 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8225 (mtp85) REVERT: A 380 SER cc_start: 0.8218 (p) cc_final: 0.7840 (p) REVERT: A 410 ASP cc_start: 0.7686 (p0) cc_final: 0.7433 (p0) REVERT: A 412 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8520 (mtmm) REVERT: A 428 MET cc_start: 0.8415 (mtt) cc_final: 0.8161 (mtt) REVERT: A 430 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8328 (ttmm) REVERT: A 436 ILE cc_start: 0.8890 (mt) cc_final: 0.8518 (tt) REVERT: A 447 THR cc_start: 0.8816 (p) cc_final: 0.8438 (t) REVERT: A 463 LYS cc_start: 0.8213 (tptm) cc_final: 0.7725 (tppp) REVERT: A 490 MET cc_start: 0.8052 (mmm) cc_final: 0.7544 (mmm) REVERT: A 572 LYS cc_start: 0.8439 (mttp) cc_final: 0.8056 (mtpp) REVERT: A 580 GLU cc_start: 0.8312 (tt0) cc_final: 0.8091 (tt0) REVERT: A 584 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 622 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7993 (mm-30) outliers start: 21 outliers final: 16 residues processed: 200 average time/residue: 0.0784 time to fit residues: 19.4097 Evaluate side-chains 209 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.142592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119586 restraints weight = 7916.927| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.09 r_work: 0.3395 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5735 Z= 0.155 Angle : 0.557 5.780 7807 Z= 0.314 Chirality : 0.044 0.150 876 Planarity : 0.004 0.057 929 Dihedral : 15.886 59.206 885 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.74 % Allowed : 18.00 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.34), residues: 624 helix: 1.50 (0.30), residues: 301 sheet: -0.20 (0.58), residues: 84 loop : 0.04 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 395 TYR 0.009 0.001 TYR A 223 PHE 0.015 0.002 PHE A 58 TRP 0.005 0.001 TRP A 512 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 5735) covalent geometry : angle 0.55669 / 0.31 ( 7807) hydrogen bonds : bond 0.04236 / 2.70 ( 290) hydrogen bonds : angle 4.59895 / 3.20 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.185 Fit side-chains REVERT: A 9 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8375 (tppt) REVERT: A 68 ASN cc_start: 0.8601 (m-40) cc_final: 0.8349 (m110) REVERT: A 74 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8343 (tptp) REVERT: A 89 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 103 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 112 MET cc_start: 0.8120 (mmt) cc_final: 0.7749 (mmt) REVERT: A 117 LYS cc_start: 0.8292 (mttm) cc_final: 0.7858 (mttm) REVERT: A 143 ASP cc_start: 0.7982 (m-30) cc_final: 0.7741 (m-30) REVERT: A 201 ASN cc_start: 0.8275 (t0) cc_final: 0.7991 (t0) REVERT: A 203 LEU cc_start: 0.8376 (mt) cc_final: 0.8102 (mp) REVERT: A 233 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 260 ASP cc_start: 0.8038 (t0) cc_final: 0.7474 (t0) REVERT: A 285 LYS cc_start: 0.7969 (mttm) cc_final: 0.7767 (mttm) REVERT: A 286 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 292 ASN cc_start: 0.8198 (t0) cc_final: 0.7788 (t0) REVERT: A 319 THR cc_start: 0.7890 (p) cc_final: 0.7584 (p) REVERT: A 323 ASN cc_start: 0.7670 (t0) cc_final: 0.7137 (t0) REVERT: A 332 GLU cc_start: 0.8192 (tp30) cc_final: 0.7933 (mm-30) REVERT: A 380 SER cc_start: 0.8201 (p) cc_final: 0.7784 (p) REVERT: A 410 ASP cc_start: 0.7667 (p0) cc_final: 0.7431 (p0) REVERT: A 412 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8415 (mtmm) REVERT: A 430 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8340 (ttmm) REVERT: A 436 ILE cc_start: 0.8898 (mt) cc_final: 0.8531 (tt) REVERT: A 447 THR cc_start: 0.8821 (p) cc_final: 0.8439 (t) REVERT: A 463 LYS cc_start: 0.8199 (tptm) cc_final: 0.7723 (tppp) REVERT: A 474 ASN cc_start: 0.8397 (t0) cc_final: 0.8003 (t0) REVERT: A 490 MET cc_start: 0.7999 (mmm) cc_final: 0.7578 (mmm) REVERT: A 572 LYS cc_start: 0.8432 (mttp) cc_final: 0.8050 (mtpp) REVERT: A 580 GLU cc_start: 0.8317 (tt0) cc_final: 0.8101 (tt0) REVERT: A 584 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 622 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7976 (mm-30) outliers start: 22 outliers final: 16 residues processed: 204 average time/residue: 0.0762 time to fit residues: 19.3593 Evaluate side-chains 211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.143802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120580 restraints weight = 7959.809| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.11 r_work: 0.3411 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5735 Z= 0.127 Angle : 0.570 7.445 7807 Z= 0.318 Chirality : 0.043 0.146 876 Planarity : 0.003 0.056 929 Dihedral : 15.839 58.998 885 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.44 % Favored : 98.40 % Rotamer: Outliers : 2.89 % Allowed : 20.03 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.34), residues: 624 helix: 1.59 (0.30), residues: 302 sheet: -0.17 (0.62), residues: 74 loop : -0.01 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 340 TYR 0.011 0.001 TYR A 339 PHE 0.025 0.002 PHE A 537 TRP 0.007 0.001 TRP A 512 HIS 0.002 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5735) covalent geometry : angle 0.56964 / 0.32 ( 7807) hydrogen bonds : bond 0.03978 / 2.53 ( 290) hydrogen bonds : angle 4.53796 / 3.16 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.201 Fit side-chains REVERT: A 9 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8373 (tppt) REVERT: A 68 ASN cc_start: 0.8560 (m-40) cc_final: 0.8345 (m110) REVERT: A 89 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 96 ARG cc_start: 0.8072 (tpt90) cc_final: 0.7720 (tpt-90) REVERT: A 103 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 117 LYS cc_start: 0.8274 (mttm) cc_final: 0.7817 (mttm) REVERT: A 143 ASP cc_start: 0.7963 (m-30) cc_final: 0.7724 (m-30) REVERT: A 201 ASN cc_start: 0.8266 (t0) cc_final: 0.7651 (t0) REVERT: A 203 LEU cc_start: 0.8394 (mt) cc_final: 0.8091 (mp) REVERT: A 233 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 260 ASP cc_start: 0.7996 (t0) cc_final: 0.7455 (t0) REVERT: A 285 LYS cc_start: 0.7917 (mttm) cc_final: 0.7716 (mttm) REVERT: A 286 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 292 ASN cc_start: 0.8126 (t0) cc_final: 0.7741 (t0) REVERT: A 319 THR cc_start: 0.7815 (p) cc_final: 0.7510 (p) REVERT: A 323 ASN cc_start: 0.7632 (t0) cc_final: 0.7116 (t0) REVERT: A 332 GLU cc_start: 0.8186 (tp30) cc_final: 0.7940 (mm-30) REVERT: A 377 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8206 (mtp85) REVERT: A 380 SER cc_start: 0.8100 (p) cc_final: 0.7666 (p) REVERT: A 410 ASP cc_start: 0.7661 (p0) cc_final: 0.7421 (p0) REVERT: A 412 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8413 (mtmm) REVERT: A 430 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8300 (ttmm) REVERT: A 436 ILE cc_start: 0.8887 (mt) cc_final: 0.8539 (tt) REVERT: A 447 THR cc_start: 0.8819 (p) cc_final: 0.8434 (t) REVERT: A 463 LYS cc_start: 0.8167 (tptm) cc_final: 0.7682 (tppp) REVERT: A 474 ASN cc_start: 0.8403 (t0) cc_final: 0.7995 (t0) REVERT: A 490 MET cc_start: 0.8057 (mmm) cc_final: 0.7683 (mmm) REVERT: A 580 GLU cc_start: 0.8320 (tt0) cc_final: 0.8097 (tt0) REVERT: A 584 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 622 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7965 (mm-30) outliers start: 17 outliers final: 12 residues processed: 203 average time/residue: 0.0751 time to fit residues: 18.9707 Evaluate side-chains 211 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN A 170 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118930 restraints weight = 7894.017| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.12 r_work: 0.3377 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5735 Z= 0.187 Angle : 0.585 7.032 7807 Z= 0.327 Chirality : 0.045 0.148 876 Planarity : 0.004 0.058 929 Dihedral : 15.815 59.064 885 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.89 % Allowed : 20.37 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.34), residues: 624 helix: 1.55 (0.30), residues: 302 sheet: -0.25 (0.58), residues: 84 loop : 0.05 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.010 0.001 TYR A 223 PHE 0.017 0.002 PHE A 58 TRP 0.006 0.002 TRP A 199 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 5735) covalent geometry : angle 0.58549 / 0.33 ( 7807) hydrogen bonds : bond 0.04264 / 2.72 ( 290) hydrogen bonds : angle 4.55207 / 3.17 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.71 seconds wall clock time: 24 minutes 20.09 seconds (1460.09 seconds total)