Starting phenix.real_space_refine on Tue Aug 4 19:10:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2026/8scz_40347.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 S 31 5.16 5 C 3853 2.51 5 N 1092 2.21 5 O 1372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Unusual residues: {'GTP': 1} Classifications: {'RNA': 59, 'undetermined': 1} Modifications used: {'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna3p': 58, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 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 4191 SG CYS A 810 60.315 59.247 80.471 1.00 37.82 S ATOM 4217 SG CYS A 813 62.572 62.668 80.179 1.00 49.69 S ATOM 4630 SG CYS A 864 59.188 62.171 82.238 1.00 46.29 S ATOM 4669 SG CYS A 869 59.417 62.787 78.708 1.00 0.00 S Time building chain proxies: 1.26, per 1000 atoms: 0.20 Number of scatterers: 6411 At special positions: 0 Unit cell: (100.392, 91.848, 111.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 62 15.00 O 1372 8.00 N 1092 7.00 C 3853 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 270.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " Number of angles added : 6 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 49.6% alpha, 9.3% beta 29 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.984A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 267 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.590A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.883A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.000A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.541A pdb=" N THR A 377 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.876A pdb=" N GLN A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.030A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.869A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 4.074A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.986A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.719A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.270A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.513A pdb=" N PHE A 371 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.730A pdb=" N THR A 322 " --> pdb=" O ILE A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 462 removed outlier: 3.569A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.888A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.469A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR A 831 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1771 1.34 - 1.46: 1611 1.46 - 1.58: 3116 1.58 - 1.70: 122 1.70 - 1.82: 43 Bond restraints: 6663 Sorted by residual: bond pdb=" C VAL A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.32e-02 5.74e+03 4.94e+00 bond pdb=" CB PRO A 626 " pdb=" CG PRO A 626 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" CB PHE A 388 " pdb=" CG PHE A 388 " ideal model delta sigma weight residual 1.502 1.541 -0.039 2.30e-02 1.89e+03 2.88e+00 bond pdb=" C ILE A 884 " pdb=" N PRO A 885 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.20e-02 6.94e+03 2.69e+00 ... (remaining 6658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8805 1.99 - 3.98: 423 3.98 - 5.97: 39 5.97 - 7.96: 12 7.96 - 9.95: 4 Bond angle restraints: 9283 Sorted by residual: angle pdb=" N1 C B 37 " pdb=" C2 C B 37 " pdb=" O2 C B 37 " ideal model delta sigma weight residual 118.90 121.81 -2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" C2 C B 5 " pdb=" N1 C B 5 " pdb=" C6 C B 5 " ideal model delta sigma weight residual 120.30 118.41 1.89 4.00e-01 6.25e+00 2.23e+01 angle pdb=" O2 C B 37 " pdb=" C2 C B 37 " pdb=" N3 C B 37 " ideal model delta sigma weight residual 121.90 118.64 3.26 7.00e-01 2.04e+00 2.17e+01 angle pdb=" C GLU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 angle pdb=" C2 C B 37 " pdb=" N1 C B 37 " pdb=" C6 C B 37 " ideal model delta sigma weight residual 120.30 118.48 1.82 4.00e-01 6.25e+00 2.07e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 3489 18.40 - 36.81: 413 36.81 - 55.21: 141 55.21 - 73.61: 84 73.61 - 92.01: 12 Dihedral angle restraints: 4139 sinusoidal: 2267 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.48 91.11 1 2.00e+01 2.50e-03 2.45e+01 dihedral pdb=" CA GLU A 373 " pdb=" C GLU A 373 " pdb=" N CYS A 374 " pdb=" CA CYS A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN A 404 " pdb=" C GLN A 404 " pdb=" N VAL A 405 " pdb=" CA VAL A 405 " ideal model delta harmonic sigma weight residual 180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 742 0.044 - 0.088: 207 0.088 - 0.132: 86 0.132 - 0.175: 45 0.175 - 0.219: 3 Chirality restraints: 1083 Sorted by residual: chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 552 " pdb=" CB LEU A 552 " pdb=" CD1 LEU A 552 " pdb=" CD2 LEU A 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 1080 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 342 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP A 342 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP A 342 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE A 343 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 800 " -0.061 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 801 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 390 " 0.016 2.00e-02 2.50e+03 2.14e-02 9.17e+00 pdb=" CG TYR A 390 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 390 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 390 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 390 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 390 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 390 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 390 " 0.000 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 21 2.45 - 3.06: 3585 3.06 - 3.67: 10435 3.67 - 4.29: 14899 4.29 - 4.90: 23675 Nonbonded interactions: 52615 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" CD1 LEU A 449 " model vdw 1.836 3.460 nonbonded pdb=" CE1 PHE A 460 " pdb=" CD2 LEU A 740 " model vdw 2.268 3.760 nonbonded pdb=" O GLN A 457 " pdb=" CD2 PHE A 459 " model vdw 2.285 3.340 nonbonded pdb=" O GLN A 511 " pdb=" OG1 THR A 515 " model vdw 2.304 3.040 nonbonded pdb=" O GLU A 583 " pdb=" OG1 THR A 587 " model vdw 2.315 3.040 ... (remaining 52610 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: 0.280 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.210 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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 0.108 6668 Z= 0.234 Angle : 0.919 13.246 9289 Z= 0.614 Chirality : 0.054 0.219 1083 Planarity : 0.006 0.094 962 Dihedral : 19.405 92.015 2919 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.22 % Favored : 93.62 % Rotamer: Outliers : 0.35 % Allowed : 27.32 % Favored : 72.33 % 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: -2.21 (0.29), residues: 627 helix: -0.88 (0.27), residues: 279 sheet: -2.03 (0.58), residues: 74 loop : -1.81 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 488 TYR 0.052 0.003 TYR A 390 PHE 0.032 0.002 PHE A 388 TRP 0.011 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.23 ( 6663) covalent geometry : angle 0.88099 / 0.61 ( 9283) hydrogen bonds : bond 0.12840 / 8.09 ( 317) hydrogen bonds : angle 5.63470 / 4.06 ( 861) metal coordination : bond 0.01676 / 0.85 ( 4) metal coordination : angle 10.39205 / 4.94 ( 6) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.129 Fit side-chains REVERT: A 279 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 469 ASP cc_start: 0.6996 (p0) cc_final: 0.6607 (p0) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.0473 time to fit residues: 4.9076 Evaluate side-chains 58 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.223736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182529 restraints weight = 6609.987| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.73 r_work: 0.3990 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6668 Z= 0.127 Angle : 0.539 8.165 9289 Z= 0.274 Chirality : 0.037 0.151 1083 Planarity : 0.004 0.055 962 Dihedral : 17.511 91.423 1614 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 1.93 % Allowed : 26.44 % Favored : 71.63 % 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: -1.23 (0.31), residues: 627 helix: 0.44 (0.29), residues: 287 sheet: -1.82 (0.55), residues: 88 loop : -1.87 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.022 0.002 TYR A 390 PHE 0.011 0.001 PHE A 388 TRP 0.005 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6663) covalent geometry : angle 0.51470 / 0.27 ( 9283) hydrogen bonds : bond 0.04725 / 3.00 ( 317) hydrogen bonds : angle 4.30187 / 3.09 ( 861) metal coordination : bond 0.00531 / 0.26 ( 4) metal coordination : angle 6.25445 / 2.99 ( 6) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.187 Fit side-chains REVERT: A 469 ASP cc_start: 0.6971 (p0) cc_final: 0.6562 (p0) REVERT: A 569 ASP cc_start: 0.7292 (t0) cc_final: 0.6598 (m-30) REVERT: A 760 MET cc_start: 0.7956 (ptm) cc_final: 0.7710 (ptm) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.0480 time to fit residues: 4.9943 Evaluate side-chains 66 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.222633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181074 restraints weight = 6549.052| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.73 r_work: 0.3970 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6668 Z= 0.107 Angle : 0.504 8.759 9289 Z= 0.249 Chirality : 0.036 0.136 1083 Planarity : 0.003 0.052 962 Dihedral : 17.371 90.635 1613 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 3.85 % Allowed : 24.34 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.33), residues: 627 helix: 1.09 (0.31), residues: 289 sheet: -1.87 (0.56), residues: 88 loop : -1.72 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.021 0.001 TYR A 390 PHE 0.012 0.001 PHE A 388 TRP 0.006 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6663) covalent geometry : angle 0.48031 / 0.25 ( 9283) hydrogen bonds : bond 0.04143 / 2.64 ( 317) hydrogen bonds : angle 4.05088 / 2.93 ( 861) metal coordination : bond 0.00369 / 0.18 ( 4) metal coordination : angle 6.07934 / 2.91 ( 6) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7329 (tp) REVERT: A 360 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5867 (mm) REVERT: A 469 ASP cc_start: 0.6968 (p0) cc_final: 0.6516 (p0) REVERT: A 479 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7425 (mtm) REVERT: A 569 ASP cc_start: 0.7303 (t0) cc_final: 0.6540 (m-30) REVERT: A 760 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7636 (ptm) outliers start: 22 outliers final: 12 residues processed: 79 average time/residue: 0.0459 time to fit residues: 5.4436 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 4 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.222177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.181032 restraints weight = 6626.129| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.70 r_work: 0.3976 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6668 Z= 0.103 Angle : 0.486 7.977 9289 Z= 0.242 Chirality : 0.036 0.140 1083 Planarity : 0.003 0.053 962 Dihedral : 17.353 89.987 1613 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 3.85 % Allowed : 23.99 % Favored : 72.15 % 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: -0.38 (0.34), residues: 627 helix: 1.38 (0.31), residues: 289 sheet: -1.90 (0.57), residues: 88 loop : -1.57 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.019 0.001 TYR A 390 PHE 0.012 0.001 PHE A 388 TRP 0.006 0.001 TRP A 771 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6663) covalent geometry : angle 0.46220 / 0.24 ( 9283) hydrogen bonds : bond 0.03907 / 2.48 ( 317) hydrogen bonds : angle 3.93277 / 2.86 ( 861) metal coordination : bond 0.00331 / 0.16 ( 4) metal coordination : angle 5.94951 / 2.85 ( 6) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.114 Fit side-chains REVERT: A 469 ASP cc_start: 0.6917 (p0) cc_final: 0.6462 (p0) REVERT: A 479 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7465 (mtm) REVERT: A 569 ASP cc_start: 0.7184 (t0) cc_final: 0.6504 (m-30) REVERT: A 760 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7633 (ptm) outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.0456 time to fit residues: 5.1055 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 340 ASN ** A 354 ASN ** 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 = 0.4414 r_free = 0.4414 target = 0.214900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174686 restraints weight = 6672.679| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.85 r_work: 0.3872 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6668 Z= 0.168 Angle : 0.562 10.356 9289 Z= 0.275 Chirality : 0.039 0.170 1083 Planarity : 0.004 0.054 962 Dihedral : 17.332 95.836 1613 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 4.73 % Allowed : 23.82 % Favored : 71.45 % 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: -0.42 (0.35), residues: 627 helix: 1.31 (0.31), residues: 290 sheet: -1.96 (0.58), residues: 87 loop : -1.54 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.034 0.002 TYR A 390 PHE 0.020 0.002 PHE A 371 TRP 0.007 0.001 TRP A 908 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6663) covalent geometry : angle 0.53346 / 0.27 ( 9283) hydrogen bonds : bond 0.04449 / 2.88 ( 317) hydrogen bonds : angle 4.05387 / 2.94 ( 861) metal coordination : bond 0.00324 / 0.16 ( 4) metal coordination : angle 7.01435 / 3.29 ( 6) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (tp) REVERT: A 469 ASP cc_start: 0.6972 (p0) cc_final: 0.6572 (p0) REVERT: A 479 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: A 569 ASP cc_start: 0.7224 (t0) cc_final: 0.6473 (m-30) REVERT: A 760 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7721 (ptm) outliers start: 27 outliers final: 16 residues processed: 83 average time/residue: 0.0485 time to fit residues: 5.6714 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.217152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175904 restraints weight = 6621.482| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.85 r_work: 0.3884 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6668 Z= 0.118 Angle : 0.520 9.492 9289 Z= 0.254 Chirality : 0.037 0.142 1083 Planarity : 0.003 0.054 962 Dihedral : 17.340 92.876 1613 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.58 % Favored : 94.26 % Rotamer: Outliers : 3.50 % Allowed : 24.52 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.35), residues: 627 helix: 1.51 (0.31), residues: 289 sheet: -1.85 (0.64), residues: 75 loop : -1.41 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.024 0.001 TYR A 390 PHE 0.015 0.001 PHE A 388 TRP 0.006 0.001 TRP A 908 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6663) covalent geometry : angle 0.48964 / 0.25 ( 9283) hydrogen bonds : bond 0.04033 / 2.58 ( 317) hydrogen bonds : angle 3.94600 / 2.86 ( 861) metal coordination : bond 0.00274 / 0.14 ( 4) metal coordination : angle 6.92754 / 3.28 ( 6) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.149 Fit side-chains REVERT: A 469 ASP cc_start: 0.6943 (p0) cc_final: 0.6535 (p0) REVERT: A 479 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7624 (mtm) REVERT: A 760 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7681 (ptm) outliers start: 20 outliers final: 14 residues processed: 70 average time/residue: 0.0504 time to fit residues: 5.1083 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.0000 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.216439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176062 restraints weight = 6613.597| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.84 r_work: 0.3889 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6668 Z= 0.124 Angle : 0.518 9.702 9289 Z= 0.253 Chirality : 0.037 0.157 1083 Planarity : 0.003 0.054 962 Dihedral : 17.340 92.566 1613 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.15 % Allowed : 25.39 % Favored : 71.45 % 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: -0.13 (0.35), residues: 627 helix: 1.53 (0.31), residues: 290 sheet: -1.86 (0.62), residues: 80 loop : -1.37 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.023 0.001 TYR A 390 PHE 0.013 0.001 PHE A 388 TRP 0.006 0.001 TRP A 908 HIS 0.002 0.001 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6663) covalent geometry : angle 0.48644 / 0.25 ( 9283) hydrogen bonds : bond 0.04032 / 2.58 ( 317) hydrogen bonds : angle 3.93156 / 2.85 ( 861) metal coordination : bond 0.00256 / 0.13 ( 4) metal coordination : angle 7.02666 / 3.33 ( 6) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6948 (p0) cc_final: 0.6537 (p0) REVERT: A 479 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7651 (mtm) REVERT: A 760 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7704 (ptm) outliers start: 18 outliers final: 15 residues processed: 68 average time/residue: 0.0507 time to fit residues: 4.9638 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.218121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178704 restraints weight = 6591.348| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.72 r_work: 0.3933 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6668 Z= 0.105 Angle : 0.502 9.846 9289 Z= 0.244 Chirality : 0.037 0.177 1083 Planarity : 0.003 0.054 962 Dihedral : 17.337 90.641 1613 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.15 % Allowed : 25.74 % Favored : 71.10 % 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: -0.03 (0.35), residues: 627 helix: 1.58 (0.31), residues: 297 sheet: -1.79 (0.63), residues: 80 loop : -1.38 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.021 0.001 TYR A 390 PHE 0.009 0.001 PHE A 371 TRP 0.005 0.001 TRP A 908 HIS 0.002 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 6663) covalent geometry : angle 0.47049 / 0.24 ( 9283) hydrogen bonds : bond 0.03843 / 2.46 ( 317) hydrogen bonds : angle 3.87073 / 2.79 ( 861) metal coordination : bond 0.00239 / 0.12 ( 4) metal coordination : angle 6.94770 / 3.32 ( 6) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.7916 (mtm) cc_final: 0.7706 (mtm) REVERT: A 469 ASP cc_start: 0.6905 (p0) cc_final: 0.6522 (p0) REVERT: A 479 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7518 (mtm) outliers start: 18 outliers final: 16 residues processed: 68 average time/residue: 0.0561 time to fit residues: 5.2833 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.215752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.175293 restraints weight = 6696.719| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.84 r_work: 0.3802 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6668 Z= 0.132 Angle : 0.525 9.898 9289 Z= 0.255 Chirality : 0.037 0.166 1083 Planarity : 0.004 0.053 962 Dihedral : 17.330 93.271 1613 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.33 % Allowed : 25.92 % Favored : 70.75 % 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: -0.09 (0.35), residues: 627 helix: 1.60 (0.31), residues: 290 sheet: -1.99 (0.61), residues: 82 loop : -1.34 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.022 0.001 TYR A 390 PHE 0.011 0.001 PHE A 371 TRP 0.007 0.001 TRP A 908 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6663) covalent geometry : angle 0.49247 / 0.25 ( 9283) hydrogen bonds : bond 0.04035 / 2.59 ( 317) hydrogen bonds : angle 3.93220 / 2.84 ( 861) metal coordination : bond 0.00308 / 0.15 ( 4) metal coordination : angle 7.22202 / 3.42 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6853 (p0) cc_final: 0.6463 (p0) REVERT: A 479 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7623 (mtm) outliers start: 19 outliers final: 16 residues processed: 68 average time/residue: 0.0557 time to fit residues: 5.3993 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.212682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171675 restraints weight = 6527.557| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.84 r_work: 0.3752 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6668 Z= 0.170 Angle : 0.592 10.782 9289 Z= 0.286 Chirality : 0.039 0.228 1083 Planarity : 0.004 0.053 962 Dihedral : 17.375 96.160 1613 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.68 % Allowed : 25.74 % Favored : 70.58 % 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: -0.28 (0.35), residues: 627 helix: 1.41 (0.31), residues: 290 sheet: -2.16 (0.61), residues: 82 loop : -1.36 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.023 0.002 TYR A 390 PHE 0.039 0.002 PHE A 388 TRP 0.010 0.001 TRP A 908 HIS 0.003 0.001 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 6663) covalent geometry : angle 0.55760 / 0.28 ( 9283) hydrogen bonds : bond 0.04310 / 2.77 ( 317) hydrogen bonds : angle 4.01122 / 2.90 ( 861) metal coordination : bond 0.00502 / 0.25 ( 4) metal coordination : angle 7.80781 / 3.68 ( 6) Misc. bond : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.140 Fit side-chains REVERT: A 469 ASP cc_start: 0.6957 (p0) cc_final: 0.6552 (p0) REVERT: A 479 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: A 525 MET cc_start: 0.3393 (ptp) cc_final: 0.3129 (ptp) REVERT: A 859 ARG cc_start: 0.6202 (mtp85) cc_final: 0.5905 (mmt180) outliers start: 21 outliers final: 20 residues processed: 71 average time/residue: 0.0664 time to fit residues: 6.5858 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.215216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174812 restraints weight = 6555.999| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.76 r_work: 0.3807 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6668 Z= 0.122 Angle : 0.546 10.874 9289 Z= 0.265 Chirality : 0.038 0.156 1083 Planarity : 0.004 0.055 962 Dihedral : 17.387 92.729 1613 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.68 % Allowed : 26.09 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.35), residues: 627 helix: 1.67 (0.31), residues: 284 sheet: -2.09 (0.60), residues: 83 loop : -1.24 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.022 0.001 TYR A 390 PHE 0.010 0.001 PHE A 371 TRP 0.007 0.001 TRP A 908 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6663) covalent geometry : angle 0.51141 / 0.26 ( 9283) hydrogen bonds : bond 0.04030 / 2.57 ( 317) hydrogen bonds : angle 3.95589 / 2.86 ( 861) metal coordination : bond 0.00300 / 0.15 ( 4) metal coordination : angle 7.55000 / 3.59 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.37 seconds wall clock time: 21 minutes 3.63 seconds (1263.63 seconds total)