Starting phenix.real_space_refine on Fri Aug 22 17:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scz_40347/08_2025/8scz_40347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scz_40347/08_2025/8scz_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_2025/8scz_40347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2025/8scz_40347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2025/8scz_40347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scz_40347/08_2025/8scz_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-2.0-5787/lib/python3.9/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: 1.30, 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: 0.35 Conformation dependent library (CDL) restraints added in 251.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 1.11 Time building geometry restraints manager: 0.46 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=" 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=" CA PRO A 626 " pdb=" N PRO A 626 " pdb=" CD PRO A 626 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" C GLN A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta sigma weight residual 120.33 123.08 -2.75 8.00e-01 1.56e+00 1.18e+01 angle pdb=" CA TYR A 390 " pdb=" CB TYR A 390 " pdb=" CG TYR A 390 " ideal model delta sigma weight residual 113.90 119.94 -6.04 1.80e+00 3.09e-01 1.13e+01 angle pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 120.83 122.88 -2.05 6.10e-01 2.69e+00 1.13e+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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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= 0.197 Angle : 0.860 13.246 9289 Z= 0.430 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 aren 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 covalent geometry : bond 0.00409 ( 6663) covalent geometry : angle 0.81870 ( 9283) hydrogen bonds : bond 0.12840 ( 317) hydrogen bonds : angle 5.63470 ( 861) metal coordination : bond 0.01676 ( 4) metal coordination : angle 10.39205 ( 6) Misc. bond : bond 0.00057 ( 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 : 0.138 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: 0.0528 time to fit residues: 5.4159 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 : 0.213 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4476 r_free = 0.4476 target = 0.222453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180340 restraints weight = 6591.296| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.74 r_work: 0.3982 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6668 Z= 0.122 Angle : 0.535 8.723 9289 Z= 0.261 Chirality : 0.036 0.143 1083 Planarity : 0.004 0.053 962 Dihedral : 17.429 91.022 1614 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 2.80 % Allowed : 25.57 % 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 aren not related in a simple way. whole: -1.13 (0.32), residues: 627 helix: 0.57 (0.30), residues: 288 sheet: -1.86 (0.56), residues: 88 loop : -1.87 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.024 0.002 TYR A 390 PHE 0.012 0.001 PHE A 856 TRP 0.005 0.001 TRP A 908 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6663) covalent geometry : angle 0.51072 ( 9283) hydrogen bonds : bond 0.03881 ( 317) hydrogen bonds : angle 4.02798 ( 861) metal coordination : bond 0.00373 ( 4) metal coordination : angle 6.24612 ( 6) Misc. bond : bond 0.00045 ( 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 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.164 Fit side-chains REVERT: A 450 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6309 (mm-30) REVERT: A 469 ASP cc_start: 0.6953 (p0) cc_final: 0.6544 (p0) REVERT: A 569 ASP cc_start: 0.7234 (t0) cc_final: 0.6462 (m-30) REVERT: A 760 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7442 (ptm) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.0559 time to fit residues: 6.1638 Evaluate side-chains 68 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 344 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4452 r_free = 0.4452 target = 0.219363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177398 restraints weight = 6581.945| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.74 r_work: 0.3940 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6668 Z= 0.120 Angle : 0.522 8.775 9289 Z= 0.251 Chirality : 0.036 0.143 1083 Planarity : 0.004 0.050 962 Dihedral : 17.327 91.163 1613 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 4.55 % Allowed : 22.77 % Favored : 72.68 % 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 aren not related in a simple way. whole: -0.53 (0.34), residues: 627 helix: 1.26 (0.31), residues: 289 sheet: -1.97 (0.56), residues: 88 loop : -1.65 (0.36), 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 0.013 0.001 PHE A 856 TRP 0.005 0.001 TRP A 771 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6663) covalent geometry : angle 0.49712 ( 9283) hydrogen bonds : bond 0.03754 ( 317) hydrogen bonds : angle 3.89708 ( 861) metal coordination : bond 0.00294 ( 4) metal coordination : angle 6.25194 ( 6) Misc. bond : bond 0.00044 ( 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 92 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.165 Fit side-chains REVERT: A 469 ASP cc_start: 0.6952 (p0) cc_final: 0.6589 (p0) REVERT: A 479 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7584 (mtm) REVERT: A 569 ASP cc_start: 0.7213 (t0) cc_final: 0.6478 (m-30) REVERT: A 760 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7685 (ptm) outliers start: 26 outliers final: 16 residues processed: 84 average time/residue: 0.0689 time to fit residues: 7.9692 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 639 LEU 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: 3.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.218283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177767 restraints weight = 6659.416| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.86 r_work: 0.3844 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6668 Z= 0.124 Angle : 0.517 8.524 9289 Z= 0.249 Chirality : 0.036 0.138 1083 Planarity : 0.003 0.048 962 Dihedral : 17.309 91.804 1613 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.58 % Favored : 94.26 % Rotamer: Outliers : 3.68 % Allowed : 25.04 % 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 aren not related in a simple way. whole: -0.13 (0.34), residues: 627 helix: 1.51 (0.31), residues: 290 sheet: -1.92 (0.61), residues: 78 loop : -1.34 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.019 0.001 TYR A 390 PHE 0.012 0.001 PHE A 856 TRP 0.006 0.001 TRP A 908 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6663) covalent geometry : angle 0.49160 ( 9283) hydrogen bonds : bond 0.03655 ( 317) hydrogen bonds : angle 3.83790 ( 861) metal coordination : bond 0.00256 ( 4) metal coordination : angle 6.37164 ( 6) Misc. bond : bond 0.00044 ( 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 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6861 (p0) cc_final: 0.6477 (p0) REVERT: A 479 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7498 (mtm) REVERT: A 569 ASP cc_start: 0.7047 (t0) cc_final: 0.6354 (m-30) REVERT: A 760 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7573 (ptm) outliers start: 21 outliers final: 11 residues processed: 74 average time/residue: 0.0654 time to fit residues: 6.7380 Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4400 r_free = 0.4400 target = 0.213709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172486 restraints weight = 6709.334| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.92 r_work: 0.3774 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6668 Z= 0.163 Angle : 0.578 9.848 9289 Z= 0.274 Chirality : 0.038 0.157 1083 Planarity : 0.004 0.047 962 Dihedral : 17.360 95.995 1613 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.06 % Favored : 93.78 % Rotamer: Outliers : 3.85 % Allowed : 25.74 % 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 aren not related in a simple way. whole: -0.21 (0.35), residues: 627 helix: 1.58 (0.31), residues: 284 sheet: -2.16 (0.58), residues: 85 loop : -1.37 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.020 0.002 TYR A 390 PHE 0.014 0.002 PHE A 371 TRP 0.008 0.001 TRP A 908 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6663) covalent geometry : angle 0.54959 ( 9283) hydrogen bonds : bond 0.04022 ( 317) hydrogen bonds : angle 3.94587 ( 861) metal coordination : bond 0.00398 ( 4) metal coordination : angle 7.08464 ( 6) Misc. bond : bond 0.00056 ( 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 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.218 Fit side-chains REVERT: A 469 ASP cc_start: 0.6912 (p0) cc_final: 0.6512 (p0) REVERT: A 479 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7471 (mtt) REVERT: A 760 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7602 (ptm) REVERT: A 859 ARG cc_start: 0.6240 (mtp85) cc_final: 0.5913 (mmt180) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.0766 time to fit residues: 7.8155 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE 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 479 MET Chi-restraints excluded: chain A residue 559 ARG 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 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: 1.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.216870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.174589 restraints weight = 6642.991| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.86 r_work: 0.3911 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2308 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= 0.114 Angle : 0.524 9.276 9289 Z= 0.248 Chirality : 0.036 0.129 1083 Planarity : 0.003 0.047 962 Dihedral : 17.374 90.507 1613 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.85 % Allowed : 25.74 % 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 aren not related in a simple way. whole: 0.07 (0.35), residues: 627 helix: 1.82 (0.31), residues: 285 sheet: -1.90 (0.60), residues: 83 loop : -1.32 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 546 TYR 0.017 0.001 TYR A 390 PHE 0.009 0.001 PHE A 371 TRP 0.005 0.001 TRP A 512 HIS 0.002 0.001 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6663) covalent geometry : angle 0.49624 ( 9283) hydrogen bonds : bond 0.03631 ( 317) hydrogen bonds : angle 3.81462 ( 861) metal coordination : bond 0.00207 ( 4) metal coordination : angle 6.64390 ( 6) Misc. bond : bond 0.00056 ( 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: 22 poor density : 60 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6850 (p0) cc_final: 0.6498 (p0) REVERT: A 479 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: A 646 TRP cc_start: 0.7314 (t60) cc_final: 0.7112 (t60) REVERT: A 859 ARG cc_start: 0.6114 (mtp85) cc_final: 0.5799 (mmt180) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.0748 time to fit residues: 7.6702 Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4388 r_free = 0.4388 target = 0.212425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170603 restraints weight = 6681.225| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.79 r_work: 0.3757 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2640 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= 0.166 Angle : 0.590 10.197 9289 Z= 0.280 Chirality : 0.038 0.193 1083 Planarity : 0.004 0.046 962 Dihedral : 17.413 96.193 1613 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.85 % Allowed : 25.74 % 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 aren not related in a simple way. whole: -0.13 (0.35), residues: 627 helix: 1.55 (0.31), residues: 290 sheet: -2.35 (0.63), residues: 71 loop : -1.28 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.020 0.002 TYR A 390 PHE 0.015 0.002 PHE A 371 TRP 0.009 0.001 TRP A 908 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6663) covalent geometry : angle 0.56224 ( 9283) hydrogen bonds : bond 0.04027 ( 317) hydrogen bonds : angle 3.94228 ( 861) metal coordination : bond 0.00385 ( 4) metal coordination : angle 7.06013 ( 6) Misc. bond : bond 0.00056 ( 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 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.211 Fit side-chains REVERT: A 469 ASP cc_start: 0.6889 (p0) cc_final: 0.6484 (p0) REVERT: A 479 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7832 (mtm) REVERT: A 646 TRP cc_start: 0.7414 (t60) cc_final: 0.7211 (t60) REVERT: A 859 ARG cc_start: 0.6302 (mtp85) cc_final: 0.5964 (mmt180) outliers start: 22 outliers final: 16 residues processed: 77 average time/residue: 0.0790 time to fit residues: 8.0282 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 479 MET Chi-restraints excluded: chain A residue 559 ARG 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 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: 6.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 44 optimal weight: 1.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.217657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.177539 restraints weight = 6648.827| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.77 r_work: 0.3812 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2562 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= 0.108 Angle : 0.533 8.928 9289 Z= 0.255 Chirality : 0.037 0.207 1083 Planarity : 0.003 0.048 962 Dihedral : 17.411 88.905 1613 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.50 % Allowed : 26.44 % 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 aren not related in a simple way. whole: 0.04 (0.35), residues: 627 helix: 1.70 (0.31), residues: 292 sheet: -2.08 (0.66), residues: 69 loop : -1.30 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 791 TYR 0.018 0.001 TYR A 390 PHE 0.011 0.001 PHE A 388 TRP 0.010 0.001 TRP A 873 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6663) covalent geometry : angle 0.50893 ( 9283) hydrogen bonds : bond 0.03618 ( 317) hydrogen bonds : angle 3.79908 ( 861) metal coordination : bond 0.00213 ( 4) metal coordination : angle 6.21366 ( 6) Misc. bond : bond 0.00054 ( 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 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.195 Fit side-chains REVERT: A 469 ASP cc_start: 0.6882 (p0) cc_final: 0.6541 (p0) REVERT: A 479 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: A 859 ARG cc_start: 0.6014 (mtp85) cc_final: 0.5713 (mmt180) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.0721 time to fit residues: 7.5720 Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 559 ARG 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 781 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.0270 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4379 r_free = 0.4379 target = 0.211133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167760 restraints weight = 6797.865| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.94 r_work: 0.3704 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2900 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= 0.188 Angle : 0.610 10.299 9289 Z= 0.294 Chirality : 0.039 0.180 1083 Planarity : 0.004 0.046 962 Dihedral : 17.450 97.047 1613 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.68 % Allowed : 26.62 % 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 aren not related in a simple way. whole: -0.17 (0.35), residues: 627 helix: 1.54 (0.31), residues: 285 sheet: -2.54 (0.57), residues: 84 loop : -1.11 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 546 TYR 0.034 0.002 TYR A 390 PHE 0.039 0.002 PHE A 388 TRP 0.014 0.002 TRP A 646 HIS 0.006 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6663) covalent geometry : angle 0.58469 ( 9283) hydrogen bonds : bond 0.04225 ( 317) hydrogen bonds : angle 3.99036 ( 861) metal coordination : bond 0.00449 ( 4) metal coordination : angle 6.90336 ( 6) Misc. bond : bond 0.00042 ( 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 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 270 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5497 (ttpp) REVERT: A 469 ASP cc_start: 0.6884 (p0) cc_final: 0.6532 (p0) REVERT: A 479 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7916 (mtm) outliers start: 21 outliers final: 17 residues processed: 71 average time/residue: 0.0690 time to fit residues: 6.6914 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 639 LEU 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 813 CYS Chi-restraints excluded: chain A residue 825 VAL 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: 0.0030 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4424 r_free = 0.4424 target = 0.216375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.173912 restraints weight = 6547.669| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.68 r_work: 0.3843 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6668 Z= 0.113 Angle : 0.539 9.389 9289 Z= 0.258 Chirality : 0.037 0.201 1083 Planarity : 0.004 0.047 962 Dihedral : 17.443 89.867 1613 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.63 % Allowed : 27.85 % Favored : 69.53 % 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 aren not related in a simple way. whole: 0.11 (0.35), residues: 627 helix: 1.77 (0.31), residues: 285 sheet: -2.24 (0.64), residues: 72 loop : -1.10 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 546 TYR 0.028 0.001 TYR A 390 PHE 0.034 0.001 PHE A 388 TRP 0.008 0.001 TRP A 873 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6663) covalent geometry : angle 0.51413 ( 9283) hydrogen bonds : bond 0.03694 ( 317) hydrogen bonds : angle 3.81270 ( 861) metal coordination : bond 0.00207 ( 4) metal coordination : angle 6.32641 ( 6) Misc. bond : bond 0.00051 ( 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 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.222 Fit side-chains REVERT: A 270 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5306 (ttpp) REVERT: A 469 ASP cc_start: 0.6842 (p0) cc_final: 0.6523 (p0) REVERT: A 479 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7682 (mtm) REVERT: A 859 ARG cc_start: 0.6072 (mtp85) cc_final: 0.5793 (mmt180) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.0896 time to fit residues: 8.2967 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 270 LYS 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 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 771 TRP Chi-restraints excluded: chain A residue 781 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4400 r_free = 0.4400 target = 0.213628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172121 restraints weight = 6646.012| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.80 r_work: 0.3809 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6668 Z= 0.151 Angle : 0.579 9.999 9289 Z= 0.279 Chirality : 0.038 0.184 1083 Planarity : 0.004 0.046 962 Dihedral : 17.450 93.920 1613 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.80 % Allowed : 27.85 % Favored : 69.35 % 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 aren not related in a simple way. whole: 0.01 (0.35), residues: 627 helix: 1.63 (0.31), residues: 284 sheet: -2.40 (0.62), residues: 74 loop : -1.03 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.031 0.002 TYR A 390 PHE 0.048 0.002 PHE A 388 TRP 0.008 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6663) covalent geometry : angle 0.55439 ( 9283) hydrogen bonds : bond 0.03932 ( 317) hydrogen bonds : angle 3.91537 ( 861) metal coordination : bond 0.00212 ( 4) metal coordination : angle 6.64701 ( 6) Misc. bond : bond 0.00043 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1340.92 seconds wall clock time: 23 minutes 41.98 seconds (1421.98 seconds total)