Starting phenix.real_space_refine on Thu Jul 2 03:18:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scz_40347/07_2026/8scz_40347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scz_40347/07_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_40347/07_2026/8scz_40347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scz_40347/07_2026/8scz_40347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8scz_40347/07_2026/8scz_40347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scz_40347/07_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-dev-6108/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: 1.32, per 1000 atoms: 0.21 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: 0.48 Conformation dependent library (CDL) restraints added in 347.0 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: 0.76 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: 1.00 Time building geometry restraints manager: 0.61 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: 8965 1.99 - 3.98: 263 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: 810 0.044 - 0.088: 198 0.088 - 0.132: 60 0.132 - 0.175: 12 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: 0.580 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: 0.020 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.070 ------------------------------------------------------------------------------- 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= 0.228 Angle : 0.860 13.246 9289 Z= 0.560 Chirality : 0.044 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 0.00409 / 0.23 ( 6663) covalent geometry : angle 0.81898 / 0.56 ( 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 : 0.219 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: 0.0563 time to fit residues: 5.7292 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 : 0.194 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.223890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.182764 restraints weight = 6611.583| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.71 r_work: 0.4004 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6668 Z= 0.126 Angle : 0.531 7.853 9289 Z= 0.271 Chirality : 0.037 0.143 1083 Planarity : 0.004 0.054 962 Dihedral : 17.561 91.359 1614 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 2.28 % Allowed : 25.74 % 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: -1.18 (0.32), residues: 627 helix: 0.47 (0.29), residues: 288 sheet: -1.81 (0.55), residues: 88 loop : -1.83 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.023 0.002 TYR A 390 PHE 0.011 0.001 PHE A 856 TRP 0.005 0.001 TRP A 771 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 6663) covalent geometry : angle 0.50823 / 0.27 ( 9283) hydrogen bonds : bond 0.04522 / 2.87 ( 317) hydrogen bonds : angle 4.28626 / 3.08 ( 861) metal coordination : bond 0.00548 / 0.27 ( 4) metal coordination : angle 6.13571 / 2.94 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 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 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.207 Fit side-chains REVERT: A 469 ASP cc_start: 0.6971 (p0) cc_final: 0.6547 (p0) REVERT: A 569 ASP cc_start: 0.7271 (t0) cc_final: 0.6581 (m-30) REVERT: A 760 MET cc_start: 0.7938 (ptm) cc_final: 0.7700 (ptm) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.0645 time to fit residues: 6.8194 Evaluate side-chains 68 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE 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 741 LEU 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: 0.8980 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.218580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.175606 restraints weight = 6580.345| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.77 r_work: 0.3851 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6668 Z= 0.145 Angle : 0.541 9.837 9289 Z= 0.267 Chirality : 0.037 0.154 1083 Planarity : 0.004 0.054 962 Dihedral : 17.434 93.562 1613 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.58 % Favored : 94.26 % Rotamer: Outliers : 4.03 % Allowed : 24.87 % 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: -0.75 (0.33), residues: 627 helix: 1.01 (0.31), residues: 289 sheet: -1.99 (0.55), 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 0.023 0.002 TYR A 390 PHE 0.016 0.002 PHE A 371 TRP 0.006 0.001 TRP A 908 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6663) covalent geometry : angle 0.51282 / 0.27 ( 9283) hydrogen bonds : bond 0.04407 / 2.82 ( 317) hydrogen bonds : angle 4.11117 / 2.97 ( 861) metal coordination : bond 0.00331 / 0.16 ( 4) metal coordination : angle 6.77879 / 3.20 ( 6) Misc. bond : bond 0.00048 / 0.03 ( 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 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7390 (tp) REVERT: A 469 ASP cc_start: 0.7031 (p0) cc_final: 0.6576 (p0) REVERT: A 479 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: A 569 ASP cc_start: 0.7297 (t0) cc_final: 0.6537 (m-30) REVERT: A 760 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7699 (ptm) outliers start: 23 outliers final: 13 residues processed: 76 average time/residue: 0.0633 time to fit residues: 6.8650 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 479 MET 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 813 CYS Chi-restraints excluded: chain A residue 825 VAL 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: 0.7980 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 354 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 = 0.4391 r_free = 0.4391 target = 0.212124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170851 restraints weight = 6689.801| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.91 r_work: 0.3740 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1915 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= 0.191 Angle : 0.595 11.537 9289 Z= 0.291 Chirality : 0.039 0.168 1083 Planarity : 0.004 0.055 962 Dihedral : 17.419 97.143 1613 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.66 % Rotamer: Outliers : 4.73 % Allowed : 25.22 % Favored : 70.05 % 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: -0.69 (0.34), residues: 627 helix: 1.10 (0.31), residues: 291 sheet: -2.24 (0.56), residues: 87 loop : -1.66 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.022 0.002 TYR A 390 PHE 0.023 0.002 PHE A 371 TRP 0.009 0.001 TRP A 908 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 6663) covalent geometry : angle 0.55959 / 0.29 ( 9283) hydrogen bonds : bond 0.04551 / 2.91 ( 317) hydrogen bonds : angle 4.16097 / 3.01 ( 861) metal coordination : bond 0.00440 / 0.22 ( 4) metal coordination : angle 8.01256 / 3.73 ( 6) Misc. bond : bond 0.00051 / 0.03 ( 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 93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.204 Fit side-chains REVERT: A 469 ASP cc_start: 0.7011 (p0) cc_final: 0.6578 (p0) REVERT: A 479 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6774 (mtp) REVERT: A 760 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7775 (ptm) outliers start: 27 outliers final: 17 residues processed: 85 average time/residue: 0.0734 time to fit residues: 8.6146 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 337 ILE 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 660 ILE 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 813 CYS Chi-restraints excluded: chain A residue 825 VAL 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 30.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.216582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175122 restraints weight = 6679.873| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.86 r_work: 0.3866 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1940 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= 0.115 Angle : 0.526 10.496 9289 Z= 0.257 Chirality : 0.036 0.139 1083 Planarity : 0.003 0.055 962 Dihedral : 17.415 92.859 1613 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 3.68 % Allowed : 25.39 % Favored : 70.93 % 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: -0.22 (0.35), residues: 627 helix: 1.53 (0.32), residues: 284 sheet: -2.24 (0.60), residues: 80 loop : -1.31 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.019 0.001 TYR A 390 PHE 0.014 0.001 PHE A 388 TRP 0.006 0.001 TRP A 512 HIS 0.004 0.001 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6663) covalent geometry : angle 0.49196 / 0.25 ( 9283) hydrogen bonds : bond 0.04086 / 2.59 ( 317) hydrogen bonds : angle 4.02455 / 2.90 ( 861) metal coordination : bond 0.00271 / 0.13 ( 4) metal coordination : angle 7.37971 / 3.52 ( 6) Misc. bond : bond 0.00065 / 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 79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6952 (p0) cc_final: 0.6509 (p0) REVERT: A 479 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7505 (mtm) outliers start: 21 outliers final: 15 residues processed: 73 average time/residue: 0.0642 time to fit residues: 6.8220 Evaluate side-chains 68 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE 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 534 ILE Chi-restraints excluded: chain A residue 574 VAL 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 843 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 67 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.216302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175699 restraints weight = 6631.678| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.82 r_work: 0.3817 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2008 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= 0.120 Angle : 0.524 9.955 9289 Z= 0.256 Chirality : 0.037 0.142 1083 Planarity : 0.003 0.054 962 Dihedral : 17.404 92.305 1613 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.20 % Allowed : 24.87 % Favored : 70.93 % 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: -0.17 (0.35), residues: 627 helix: 1.54 (0.32), residues: 290 sheet: -2.00 (0.61), residues: 80 loop : -1.42 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.020 0.001 TYR A 390 PHE 0.013 0.001 PHE A 388 TRP 0.006 0.001 TRP A 873 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6663) covalent geometry : angle 0.49222 / 0.25 ( 9283) hydrogen bonds : bond 0.03988 / 2.54 ( 317) hydrogen bonds : angle 3.97039 / 2.87 ( 861) metal coordination : bond 0.00209 / 0.10 ( 4) metal coordination : angle 7.07199 / 3.40 ( 6) Misc. bond : bond 0.00055 / 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 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.203 Fit side-chains REVERT: A 469 ASP cc_start: 0.6982 (p0) cc_final: 0.6571 (p0) REVERT: A 479 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7694 (mtm) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.0555 time to fit residues: 6.1625 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.216314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174857 restraints weight = 6657.590| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.81 r_work: 0.3818 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6668 Z= 0.125 Angle : 0.532 9.764 9289 Z= 0.259 Chirality : 0.037 0.175 1083 Planarity : 0.004 0.054 962 Dihedral : 17.389 92.426 1613 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.03 % Allowed : 25.57 % Favored : 70.40 % 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: -0.14 (0.35), residues: 627 helix: 1.54 (0.31), residues: 290 sheet: -2.00 (0.63), residues: 75 loop : -1.37 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.018 0.001 TYR A 390 PHE 0.014 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 0.00283 / 0.12 ( 6663) covalent geometry : angle 0.50197 / 0.26 ( 9283) hydrogen bonds : bond 0.04002 / 2.56 ( 317) hydrogen bonds : angle 3.96533 / 2.86 ( 861) metal coordination : bond 0.00201 / 0.10 ( 4) metal coordination : angle 6.98376 / 3.36 ( 6) Misc. bond : bond 0.00050 / 0.03 ( 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 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6978 (p0) cc_final: 0.6572 (p0) REVERT: A 479 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7606 (mtm) outliers start: 23 outliers final: 18 residues processed: 71 average time/residue: 0.0655 time to fit residues: 6.5424 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.217069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175915 restraints weight = 6655.175| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.80 r_work: 0.3823 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6668 Z= 0.113 Angle : 0.519 9.534 9289 Z= 0.251 Chirality : 0.037 0.164 1083 Planarity : 0.003 0.053 962 Dihedral : 17.380 91.449 1613 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.03 % Allowed : 24.69 % Favored : 71.28 % 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: -0.02 (0.35), residues: 627 helix: 1.67 (0.31), residues: 291 sheet: -1.89 (0.64), residues: 75 loop : -1.39 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.018 0.001 TYR A 390 PHE 0.009 0.001 PHE A 882 TRP 0.006 0.001 TRP A 873 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6663) covalent geometry : angle 0.49005 / 0.25 ( 9283) hydrogen bonds : bond 0.03891 / 2.48 ( 317) hydrogen bonds : angle 3.91803 / 2.82 ( 861) metal coordination : bond 0.00207 / 0.10 ( 4) metal coordination : angle 6.79857 / 3.28 ( 6) Misc. bond : bond 0.00050 / 0.03 ( 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 80 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6966 (p0) cc_final: 0.6537 (p0) REVERT: A 479 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7599 (mtm) outliers start: 23 outliers final: 18 residues processed: 74 average time/residue: 0.0664 time to fit residues: 6.9232 Evaluate side-chains 72 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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 555 SER 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 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: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.213465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171758 restraints weight = 6766.551| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.94 r_work: 0.3771 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6668 Z= 0.162 Angle : 0.561 10.340 9289 Z= 0.274 Chirality : 0.038 0.184 1083 Planarity : 0.004 0.054 962 Dihedral : 17.377 94.646 1613 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.03 % Allowed : 25.22 % 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: -0.18 (0.35), residues: 627 helix: 1.49 (0.31), residues: 290 sheet: -2.18 (0.63), residues: 77 loop : -1.31 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.036 0.002 TYR A 390 PHE 0.018 0.002 PHE A 388 TRP 0.008 0.001 TRP A 908 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6663) covalent geometry : angle 0.53155 / 0.27 ( 9283) hydrogen bonds : bond 0.04237 / 2.75 ( 317) hydrogen bonds : angle 3.99248 / 2.88 ( 861) metal coordination : bond 0.00283 / 0.14 ( 4) metal coordination : angle 7.12728 / 3.40 ( 6) Misc. bond : bond 0.00035 / 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 80 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.219 Fit side-chains REVERT: A 469 ASP cc_start: 0.6897 (p0) cc_final: 0.6523 (p0) REVERT: A 479 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7503 (mtm) REVERT: A 859 ARG cc_start: 0.6204 (mtp85) cc_final: 0.5880 (mmt180) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.0633 time to fit residues: 6.4665 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 337 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN 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 555 SER 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 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: 6.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.214055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172561 restraints weight = 6564.615| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.87 r_work: 0.3786 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2414 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= 0.146 Angle : 0.553 10.342 9289 Z= 0.269 Chirality : 0.038 0.147 1083 Planarity : 0.004 0.054 962 Dihedral : 17.406 94.083 1613 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.85 % Allowed : 25.92 % 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: -0.19 (0.35), residues: 627 helix: 1.48 (0.31), residues: 290 sheet: -2.20 (0.62), residues: 77 loop : -1.30 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.031 0.002 TYR A 390 PHE 0.047 0.002 PHE A 388 TRP 0.008 0.001 TRP A 908 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6663) covalent geometry : angle 0.52143 / 0.27 ( 9283) hydrogen bonds : bond 0.04138 / 2.65 ( 317) hydrogen bonds : angle 3.99826 / 2.89 ( 861) metal coordination : bond 0.00246 / 0.12 ( 4) metal coordination : angle 7.20640 / 3.45 ( 6) Misc. bond : bond 0.00051 / 0.03 ( 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 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.209 Fit side-chains REVERT: A 469 ASP cc_start: 0.6944 (p0) cc_final: 0.6571 (p0) REVERT: A 479 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7530 (mtm) REVERT: A 859 ARG cc_start: 0.6220 (mtp85) cc_final: 0.5909 (mmt180) outliers start: 22 outliers final: 19 residues processed: 74 average time/residue: 0.0682 time to fit residues: 7.1657 Evaluate side-chains 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN 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 555 SER 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 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: 3.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 40.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.215531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173412 restraints weight = 6623.097| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.88 r_work: 0.3809 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2413 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= 0.123 Angle : 0.538 10.054 9289 Z= 0.264 Chirality : 0.038 0.141 1083 Planarity : 0.004 0.055 962 Dihedral : 17.413 92.371 1613 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.85 % Allowed : 26.44 % Favored : 69.70 % 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: -0.06 (0.35), residues: 627 helix: 1.58 (0.31), residues: 291 sheet: -2.28 (0.62), residues: 76 loop : -1.19 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.030 0.001 TYR A 390 PHE 0.012 0.001 PHE A 882 TRP 0.006 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6663) covalent geometry : angle 0.50826 / 0.26 ( 9283) hydrogen bonds : bond 0.04078 / 2.58 ( 317) hydrogen bonds : angle 3.96286 / 2.85 ( 861) metal coordination : bond 0.00198 / 0.10 ( 4) metal coordination : angle 7.00909 / 3.38 ( 6) Misc. bond : bond 0.00056 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.41 seconds wall clock time: 26 minutes 25.60 seconds (1585.60 seconds total)